7-deazapurine (pyrrolo[2,3- d]pyrimidine) 2 ... organic chemistry, 2012, 16, 161-223 161...

Current Organic Chemistry, 2012, 16, 161-223 161

1875-5348/12 $58.00+.00 © 2012 Bentham Science Publishers

7-Deazapurine (Pyrrolo[2,3-d]pyrimidine) 2’-Deoxyribonucleosides: Syntheses and

Transformations

Frank Seela,1,2

* Simone Budow1 and Xiaohua Peng

1

1Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster,

Germany and 2Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastraße

7, 49069 Osnabrück, Germany

Abstract: This review reports on the synthesis of 7-deazapurine (pyrrolo[2,3-d]pyrimidine) 2’-deoxyribonucleosides, including -D- and

-L-enantiomers, fluoro derivatives, and 2’,3’-dideoxyribonucleosides. It covers the various aspects of convergent nucleoside synthesis.

Stereochemically defined -D and -L 2’-deoxyribonucleosides as well as sugar derivatives were prepared by nucleobase anion glycosy-

lation. This glycosylation reaction is regioselective for the pyrrole nitrogen and stereoselective for -nucleoside formation. Common gly-

cosylation protocols lead to 7-deazapurine 2’-deoxyribonucleosides with unusual glycosylation sites. 7-Deazapurine 2’,3’-

dideoxyribonucleosides were also obtained from 2’-deoxy- or 3’-deoxyribonucleosides by Barton-McCombie deoxygenation, by elimina-

tion of sugar hydroxyl groups or by anion glycosylation. Another aspect of the review is the functionalization of pyrrolo[2,3-d]pyrimidine

nucleosides. A broad range of reporter groups were introduced by the Sonogashira cross coupling or the copper(I)-catalyzed Huisgen-

Meldal-Sharpless “click” reaction. The application of 7-deazapurine nucleosides as antiviral or anticancer agents, and the use of 7-

deazapurine nucleoside triphosphates in the Sanger dideoxy DNA-sequencing are also reported.

Keywords: 7-Deazapurine, pyrrolo[2,3-d]pyrimidines, nucleosides, glycosylation, enantiomers, halogenation, cross-coupling, click reaction,

triphosphates, sequencing.

1. INTRODUCTION

7-Deazapurine (pyrrolo[2,3-d]pyrimidine) 2’-deoxyribonucle-

osides and their derivatives have found widespread applications in

chemistry, physics, and biology [1-6]. In contrast to the naturally

occurring 7-deazapurine ribonucleosides [3, 5, 7], the correspond-

ing 2'-deoxyribonucleosides are not found in nature. However, a

few deoxyribonucleosides with very particular sugar structure have

been isolated from natural sources. Kanagawamicin (1, AB-116)

was obtained from Actinoplanes kanagawaensis [8], and 5’-deoxy-

7-iodotubercidin (2) [9] as well as the mycalisines A (3a) and B

(3b) [10] were identified in marine organisms (Fig. 1). (If not oth-

erwise stated purine numbering is used throughout the review).

However, no “true” 7-deazapurine 2’-deoxyribonucleoside with the

general structure of motif I was found in nature.

*Address correspondence to this author at the Laboratory of Bioorganic Chemistry and

Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster,

Germany; Tel: +49 (0)251 53406 500; Fax: +49 (0)251 53406 857; E-mail:

[email protected], Homepage: www.seela.net

Current address of X. Peng: Department of Chemistry and Biochemistry, University of

Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211,

United States.

It had been recognized that the shape of 7-deazapurine 2’-

deoxyribonucleosides resembles closely to that of purine nucleo-

sides found in duplex DNA [6, 11, 12]. Stable Watson-Crick base

pairs are formed between 7-deazapurines and complementary

pyrimidines within oligonucleotide duplexes, showing similar base

stacking as those of canonical DNA bases (Fig. 2, motifs II and III).

Substituents introduced at the 7-position of 7-deazapurine nucleo-

sides do not change the conformation around the glycosylic bond

significantly while 8-substituents of purines force the nucleosides

into the syn-conformation [13-15]. 7-Substituted purines are posi-

tively charged, while 7-substituted 7-deazapurines are neutral being

well accepted by DNA polymerases [13-15]. Bulky substituents

introduced at the 7-position of the 7-deazapurine base within the

oligonucleotide chain are well accommodated in the major groove

of B-DNA. This position is also suitable for the introduction of

reporter groups in DNA with the use of building blocks such as

triphosphates or phosphoramidites. While the latter are employed in

solid-phase oligonucleotide synthesis, the former are substrates of

DNA polymerases [11, 12, 16-18]. 7-Deazapurine nucleoside

O

HO OH

N

N N

H3C

NH2 I

2

O

HO

HN

N N

HO

O

H2N

COMe

O

R

1: R = NH2

O

MeO OH

N

N N

RCN

3a: R = NH2

b: R = OH

systematic numberingpurine numbering

1

2

3

45

6

7

4a

7a

1

2

3

4

56

7

8

9

O

HO

N

N N

HO

R

R

R = various substituents

R

R

Motif I

Fig (1). Structures of naturally occurring 7-deazapurine deoxyribonucleosides and general formula of 7-deazapurine 2’-deoxyribonucleosides.

162 Current Organic Chemistry, 2012, Vol. 16, No. 2 Seela et al.

triphosphates such as 7-deaza-2'-deoxyadenosine triphosphate

(c7dATP) and 7-deaza-2'-deoxyguanosine triphosphate (c

7dGTP, 4)

are efficiently incorporated in the growing DNA chain [16]. Com-

pound 4 can replace dGTP in the Sanger dideoxy sequencing when

dG-dC rich DNA-fragments have to be resolved by electrophoresis

[19, 20]. Corresponding 7-deazapurine 2’,3’-dideoxyribonucleoside

triphosphates, as compound 5, are utilized as fluorescent chain ter-

minators in automated sequencing machines [21, 22].

Contrary to purine 2’-deoxyribonucleosides, the 7-deazapurine

nucleosides are extremely stable at their N-glycosyl bond. Glycosyl

bond cleavage does not take place in strong acid even at elevated

temperatures; instead isomerization of the sugar moiety is observed

yielding anomeric mixtures of furanosides and pyranosides [23].

Due to the high stability of the glycosylic bond, the 7-deaza-2’-

deoxyadenosine derivative 6b of the Ca2+

-mobilizing second mes-

senger cyclic adenosine 5’-diphosphate ribose (cADPR; 6a) was

synthesized as a hydrolysis-resistant agonist candidate (Fig. 3) [24];

however its biological activity needs to be evidenced. Moreover,

the glycosylic bond stability of 7-deazapurine nucleosides has been

exploited to overcome depurination reactions occurring during

MALDI-TOF mass spectrometry thereby leading to better detection

sensitivity [25]. 7-Deazapurine nucleosides such as 7-deaza-2'-

deoxyguanosine (c7Gd) or 7-deaza-2'-deoxyisoguanosine (c

7iGd) are

more easily oxidized than their purine counterparts. Quenching of

fluorescent dyes e.g. DNA-bound ethidium bromide has been ob-

served in oligonucleotide duplexes containing c7Gd, c

7iGd, or their

7-substituted derivatives [26, 27]. This phenomenon was used to

study the electron transfer within duplex DNA. Very recently, al-

kynylated 7-deazapurine nucleosides were employed in cross-

linking reactions utilizing the copper-catalyzed azide-alkyne Huis-

gen-Meldal-Sharpless cycloaddition “click” reaction.

The widespread applicability of 7-deazapurine nucleosides in

chemistry, physics, and biology has generated intensive studies on

their synthesis and incorporation into nucleic acids. These topics

have already been subjects of several reviews [1-6, 12, 28-32],

which include the synthesis of 7-deazapurine ribonucleosides [31]

and of oligonucleotides containing 7-deazapurines as monomeric

constituents [12]. The current review focuses on the convergent

syntheses of 7-deazapurine (pyrrolo[2,3-d]pyrimidine) 2’-

deoxyribonucleosides and describes various glycosylation protocols

which make use of activated 2'-deoxyribofuranose derivatives. The

review includes work on 7-deazapurine 2’-deoxy- -D-

ribonucleosides and -L-enantiomers; it also reports on fluoronu-

cleosides and 2’,3’-dideoxyribonucleosides. Transformation reac-

tions, leading to 7-halogenated derivatives which stabilize duplex

DNA are described along with the conversion into 7-alkynyl deriva-

tives by the Sonogashira cross coupling reaction. Functionalization

of alkynylated 7-deazapurine nucleosides by the copper-catalyzed

Huisgen-Meldal-Sharpless “click” reaction with various reporter

groups and cross-linking of alkynyl 7-deazapurine nucleosides are

also covered by this review.

2. GENERAL COMMENTS ON THE CONVERGENT SYN-

THESIS OF 7-DEAZAPURINE NUCLEOSIDES

In 1983, our laboratory developed the method for the stereose-

lective nucleobase anion glycosylation which was exemplified by

the 7-deazapurine system [33, 34]. Initially, the synthesis of 7-

deazapurine nucleosides was encountered with difficulties due to

the low nucleophilicity of the 7-deazapurine pyrrole nitrogen for

electrophilic glycosylation reactions. Thus, the inertness of the pyr-

N

N

N

N

N

O

N

H

H

CH3

N

N

O

N

N

N

N

N O

H

CH3

O

H

H

H

H

H

Motif II: 'c7Ad' - dT (aps) Motif III: 'c7Gd' - dC (aps)

major groove

minor groove

RR

major groove

minor groove

O

HN

N N

O

O

H2N

4HO

POPOPHO

O O O

OH OH OH

O

N

N N

O

NH2

POPOPHO

O O O

OH OH OH

CH2NH DYE

5

R = variable substituents

Fig (2). Watson-Crick base pairs formed by 7-deazapurines and pyrimidine bases in anti-parallel stranded (aps) duplexes (upper part); 7-deazapurine triphos-

phates used in the Sanger dideoxy sequencing (lower part).

N

N

X

NH2

N 6a: X = N, R = OH

b: X = CH, R = H

O

O

OH

O

P

OP

O

HO

HO

OO

O

O

R

Fig (3).

7-Deazapurine (Pyrrolo[2,3-d]pyrimidine) 2’-Deoxyribonucleosides Current Organic Chemistry, 2012, Vol. 16, No. 2 163

role nitrogen directs the glycosylation towards the pyrimidine moi-

ety or takes place on the more nucleophilic pyrrole carbons. This

problem was overcome by generating the pyrrolyl anion which is

highly reactive and allows glycosylation at ambient temperature.

Consequently, the anomerically defined sugar halides employed in

the glycosylation do not isomerise. The generation of the pyrrolyl

anion was originally applied to ribonucleoside synthesis [35, 36].

Later, it was used by our laboratory to synthesize 7-deazapurine

arabinonucleosides [37], and presently we employ this method in

the synthesis of 7-deazapurine 2’-deoxyribonucleosides.

The stereoselective nucleobase anion glycosylation [33, 34, 38],

which is now the most widely used protocol for the synthesis of

purine or purine related 2'-deoxyribonucleosides, utilizes sugar

halides with defined configuration at the anomeric center. As sev-

eral sugar halides (halogenoses) are accessible as pure -D- or -L-

anomers, the synthesis of 7-deazapurine 2’-deoxyribonucleosides

proceeds under stereochemical control with the exclusive formation

of -D-2’-deoxyribonucleosides or -L-2’-deoxyribonucleosides. A

large number of 7-deazapurine nucleosides have been synthesized

under these conditions [30, 38, 39]. Many of them show antiviral or

anticancer activity and several have been incorporated into oligonu-

cleotides [12].

3. SYNTHESIS OF 7-DEAZAPURINE – PYRROLO[2,3-

d]PYRIMIDINE – 2’-DEOXYRIBONUCLEOSIDES

A few 7-deazapurine 2’-deoxyribonucleosides, such as 7-deaza-

2’-deoxyadenosine, were prepared from the naturally occurring

ribonucleosides by chemical deoxygenation (see section 3.3) or by

reduction of nucleoside triphosphates with ribonucleotide reductase

from Lactobacillus leichmannii [40]. These routes are only applica-

ble to 7-deazapurine 2’-deoxyribonucleosides when corresponding

ribonucleosides are available. Thus, considerable efforts have been

devoted towards their convergent synthesis. After the nucleobase

anion glycosylation was developed by our laboratory, 7-

deazapurine 2’-deoxyribonucleosides became easily accessible. The

generation of the nucleobase anion, which is the key step in the

stereocontrolled glycosylation, can be performed in different ways:

(a) the anion is formed at the interphase of a bi-layered mixture of

aqueous NaOH and an organic solvent in the presence of a quater-

nary ammonium salt (liquid-liquid conditions); (b) the anion is

generated in the organic solvent (MeCN) in the presence of pow-

dered KOH containing 15% of water using a phase-transfer catalyst

such as tris-[2-(2-methoxyethoxy)ethyl]amine (TDA-1) (solid-

liquid conditions); (c) the nucleobase is suspended or dissolved in

MeCN, and the anion is generated with NaH (sodium salt glycosy-

lation). As halogenoses, 2-deoxy-3,5-di-O-(p-toluoyl)- -D-erythro-

pentofuranosyl chloride (7) and the corresponding -L-enantiomer

8 were employed for the glycosylation. Both are stereochemically

assigned -anomers and can be isolated as crystalline compounds

(Fig. 4). The halogenose 7 was first described by Hoffer [41] and its

L-enantiomer 8 by orm [42]. The reaction time of the glycosyla-

tion should be short (15-60 min), and the reaction temperature

should be kept below 25°C to avoid anomerization of the halo-

genose.

87

O

TolO

TolO

Cl

O

OTol

OTol

Cl

Fig (4).

3.1. Nucleobase Anion Glycosylation Performed under Liquid-

liquid Conditions

This glycosylation reaction is performed in a biphasic mixture

of saturated aq. NaOH or KOH (as aqueous phase) and an organic

phase (usually dichloromethane or benzene) containing the halo-

genose and a quaternary ammonium salt as phase-transfer catalyst.

The reaction mixture is stirred with a vibromixer. It was observed

that the anomeric ratio can be changed by the concentration of so-

dium hydroxide or by the amount of phase-transfer catalyst used

during the glycosylation. Both have an influence on the reaction

rate and therefore on the anomeric ratio [43, 44]. The first conver-

gent synthesis of a 7-deazapurine 2’-deoxyribonucleoside under

stereocontrolled conditions utilizing this protocol employed 50%

aq. NaOH, benzene/dimethoxyethane and Aliquat 336 (methyltrioc-

tylammonium chloride) as a phase-transfer catalyst [33].

Glycosylation of 2-amino-7-deaza-6-methoxypurine (9) [45]

with the sugar chloride 7 furnished the anomerically pure 2-amino-

7-deaza-6-methoxypurine -D-nucleoside 10 (Scheme 1) [33]. This

N

N

OMe

H2N

N

N NH

OMe

H2N

O

HO

N

HO

+

9 7

11a

HN

N

O

H2N

O

HO

N

HO

12a

Aliquat 336, 50% aq. NaOH,

benzene/dimethoxyethane

sodium p-thiocresolate,

hexamethylphosphoric

triamide, toluene

48% 91%

N

N

OMe

H2N

O

TolO

N

TolO

10

aq. NH3

O

TolO

TolO

Cl

Scheme 1.


compound was deblocked with aq. ammonia to give the methoxy

nucleoside 11a (48% yield); 37% of nucleobase 9 was recovered.

The methoxy group of 11a was displaced with sodium p-

thiocresolate [46] in hexamethylphosphoric triamide/toluene under

nitrogen atmosphere furnishing 7-deaza-2’-deoxyguanosine (12a)

in 91% yield. The glycosylation reaction was regioselective for

nitrogen-9 and proceeds to inversion of configuration. As the crys-

talline halogenose 7 was the pure -D-anomer, the -D-nucleoside

was formed exclusively.

The conditions described above were applied later to the syn-

thesis of a series of 7-deazapurine 2’-deoxyribonucleosides. 7-

Deaza-2’-deoxy-7-methylguanosine (13) [47], 2'-deoxytubercidin

(14a) [48], 7-deaza-2’-deoxyinosine (15a) [49], 7-deaza-2’-

deoxynebularine (16a) and its 2-substituted derivatives 16b,c [50-

52], 7-deaza-2’-deoxy-6-thioguanosine (17) [53], 2-amino-2’-

deoxytubercidin (18a) [53] (Fig. 5) and related nucleosides were

prepared by our laboratory and others.

2’-Deoxytubercidin (14a) was synthesized according to Scheme

2. The glycosylation of nucleobase 19 [54] with halogenose 7 pro-

duces the -D-anomer 20 exclusively [48]. Alkaline deblocking of

the sugar protecting groups of 20 yielded 2’-deoxy-2-

methylthiotubercidin (21). Desulfurization with Raney-Nickel cata-

lyst afforded 2’-deoxytubercidin (14a).

7-Deaza-2’-deoxyinosine (15a) was prepared by the same route

(Scheme 3). Glycosylation of compound 22 [37] with 7 performed

in CH2Cl2 in the presence of 50% aq. NaOH and PhCH2(Et)3NCl

was followed by deprotection, leading to the formation of -D-

nucleoside 23 [49]. The cleavage of the 6-methoxy group was per-

formed with hydrochloric acid yielding the methylthio nucleoside

24, which after desulfurization (Raney-Nickel catalyst), gave 7-

deaza-2’-deoxyinosine (15a). As the N-glycosyl bond of 7-

dezapurine 2’-deoxyribonucleosides is rather stable, acidic condi-

tions can be used for the cleavage of the methyl group. However, in

some cases, strong acid can lead to the isomerization of the sugar

moiety [23]. In such cases, conversion under alkaline conditions is

performed. Different to the imidazole ring of the purine skeleton,

the pyrrole ring of pyrrolo[2,3-d]pyrimidine is not opened in the

presence of strong base.

Similarly, 7-deaza-2’-deoxynebularine (16a), its 2-methylthio

(16b), and the 2-amino derivative 16c have been prepared via liq-

uid-liquid phase-transfer glycosylation of 25a, 25b, and 25c, re-

spectively, employing halogenose 7 (Scheme 4) [50-52]. Due to its

high hydrophilicity, the glycosylation of 25a was carried out in

THF, and formation of an anomeric mixture (26a and its -anomer)

was observed, while the corresponding reactions of 25b and 25c

were performed in CH2Cl2 and gave almost exclusively the -D-

HN

N

O

H2N

O

HO

N

HO

13

N

N

NH2

O

HO

N

HO

14a

HN

N

O

O

HO

N

HO

15a

Me

N

N

O

HO

N

HO

R

16a: R = H

b: R = SCH3

c: R = NH2

N

N

NH2

O

HO

N

HO

18a

H2N

HN

N

S

H2N

O

HO

N

HO

17

Fig (5).

N

N

NH2

H3CS

N

N NH

NH2

H3CSO

TolO

N

TolO

19 7

20

PhCH2(Et)3NCl, 50% aq. NaOH,

benzene/dimethoxyethane

40%

79%

1M NaOMe/MeOH

N

N

NH2

H3CS

O

HO

N

HO

21

N

N

NH2

O

HO

N

HO

14a

Ra-Ni, N,N-dimethylacetamide (DMA)

67%

+O

TolO

TolO

Cl

Scheme 2.


anomers 26b,c accompanied by an increased glycosylation yield.

The increased yields of nucleosides 26b and 26c can be attributed

to the better solubility of the nucleobases 25b,c in CH2Cl2. Depro-

tection of compounds 26a-c afforded nucleosides 16a-c. Compound

16c is highly fluorescent with a quantum yield of = 0.47. The

fluorescence spectrum of 16c is shown in Fig (6). The emission

maximum of 16c is located at 395 nm upon excitation at 311 nm

[55].

Glycosylation of 2-amino-6-chloro-7-deazapurine (27a) with

halogenose 7 was performed under liquid-liquid conditions

(CH2Cl2/30% KOH/tBu4NHSO4) to yield -D-nucleoside 28a

(Scheme 5). The latter was deprotected to give 29a, which was

further aminated (NH3/MeOH) furnishing 2-amino-7-deaza-2’-

deoxyadenosine (18a). Nucleophilic displacement of the 6-chloro

substituent of 28a by a mercapto group resulted in the formation of

6-thionucleoside 30. Deprotection furnished 7-deaza-2'-deoxy-6-

thioguanosine (17) [53]. Very recently, thionucleoside 17, as a con-

stituent of single-stranded oligonucleotides, was used as a molecu-

lar anchor for gold nanoparticles (AuNPs). The covalent attachment

of 17 via the thiol group makes use of the strong affinity of the

sulphur atom for the noble metal gold. This method was employed

for the preparation of oligonucleotide gold nanoparticle conjugates

[56].

N

N

OCH3

H3CS

N

N NH

OCH3

H3CS

O

HO

N

HO

22

723

(i) 50% aq. NaOH,

PhCH2(Et)3NCl,

CH2Cl2

(ii) NaOMe/MeOH

40% 60%

HN

N

O

H3CS

O

HO

N

HO

24

HN

N

O

O

HO

N

HO

15a

Ra-Ni,

DMA

48%+

7N HCl

O

TolO

TolO

Cl

Scheme 3.

7

O

TolO

TolO

Cl

N

NRN

N NH

RO

TolO

N

TolO

25a-c

26a-c

50% aq. NaOH,

PhCH2(Et)3NCl,

a: THF; b, c: CH2Cl2

a: 36%

b: 70%

c: 77%

+

N

NR

O

HO

N

HO

16a-c

a: R = H; b: R = SCH3; c: R = NH2

NaOMe,

MeOH

Scheme 4.

Fig (6). Fluorescence spectra of the nebularine derivative 16c in water. The concentration of 16c was 10-5

M.

N

NH2N

O

HO

N

HO

16c


3.2. Nucleobase Anion Glycosylation Performed Under Solid-

Liquid Conditions

The glycosylation yields obtained under liquid-liquid conditions

were limited to 40-50% and depended very much on the solubility

of the nucleobases. When lipophilic nucleobases were used, the

yields were acceptable and the -D anomers were the only glycosy-

lation products. The situation changed when more hydrophilic nu-

cleobases, such as 7-deazapurine (25a) or 2-amino-6-chloro-7-

deazapurine (27a) were used [34]. Unfavorable partition between

the organic and the aqueous phase led to an extension of the reac-

tion time resulting in partial sugar deprotection. Side reactions were

observed on the nucleobase as well as on the halogenose 7. Under

strongly alkaline conditions, the nucleophilic substitution took

place in dichloromethane and two nucleobases were linked by a

methylene group via the pyrrole nitrogen resulting in the formation

of bis-(pyrrolo[2,3-d]pyrimidines) such as 31 (Scheme 6) [57, 58].

The second side reaction is due to the partial deprotection of the

sugar moiety. The anion of the protecting group (4-methylbenzoate)

acts as nucleophile and competes with the nucleobase anion in the

glycosylation reaction thereby forming the tris-toluoylated sugars

32a and 32b (Scheme 7) [53]. These reactions consume the halo-

genose 7 as well as the nucleobases, and reduce the glycosylation

yield.

Consequently, the protocol was changed. Powdered KOH was

employed as reagent for the nucleobase anion generation, MeCN as

solvent, and the cryptand, tris-[2-(2-methoxyethoxy)ethylamine

(TDA-1) [59] was selected as catalyst. TDA-1 is an aminopolyether

and combines properties of an amine with those of a crown ether. It

forms cavities in anhydrous aprotic solvents such as MeCN, thereby

chelating monovalent and divalent cations as well as transition

metal salts. TDA-1 shows great complex affinities for ionic com-

pounds containing large polarizable anions, e.g. nucleobase anions.

Powdered KOH contains 15% of water which is able to form an

interphase between the solid and the liquid phase thereby promoting

the glycosylation reaction. In most cases, the reaction was carried

out at room temperature. Instead of powdered KOH, sodium- or

cesium hydroxides or carbonates are sometimes advantageous as

well as organic bases (DBU). The glycosylation performed under

solid-liquid conditions results in significantly higher yields than

those obtained in the liquid-liquid system. For instance, the glyco-

sylation of nucleobase 27a with halogenose 7 formed compound

N

N

Cl

H2N

N

N NH

Cl

H2N

O

TolO

N

TolO

27a

28a

N

N

Cl

H2N

O

HO

N

HO

29a

N

N

NH2

H2N

O

HO

N

HO

18a

NaOMe,

MeOH

68%

thiourea,

1-propanol

79% 63%

NH3,

MeOH

HN

N

S

H2N

O

TolO

N

TolO

30

NaOMe,

MeOH

17

58%

+

7

tBu4NHSO4,

30% KOH,

CH2Cl2

45%O

TolO

TolO

Cl

Scheme 5.

N

N N

OMe

H3CS

31

N

NN

OMe

SCH3

N

N NH

OMe

H3CS

22

CH2Cl2,

aq. NaOH

+ CH2Cl2

Scheme 6.

+

C

CH3

O

O

32a7

O

TolO

TolO

Cl

O

TolO

TolO

+

OTol

32b

O

TolO

TolO

OTol

Scheme 7.


28a in 45% yield under liquid-liquid conditions, but proceeds with

70% yield under solid-liquid conditions [34].

Some nucleobases are particularly useful starting materials, as

the glycosylation products can be employed as common intermedi-

ates for the synthesis of a number of 7-deazapurine 2'-

deoxyribonucleosides bearing various substituents at the nucleobase

moiety. Examples are compounds 27a and 33a (Scheme 8). Both

chlorinated 7-deazapurine bases are excellent substrates for the

solid-liquid glycosylation (TDA-1/KOH/MeCN). When employing

halogenose 7, compound 28a is obtained in 70% [34] and com-

pound 34a in 81% yield [60, 61]. Compound 28a can be used to

access 7-deazapurine 2'-deoxyribonucleosides related to dG, its 6-

thio derivative, 2-amino-dA, 2’-deoxyxanthosine, and isoGd (see

section 3.2.1). The 6-chloro nucleoside 34a functions in an analo-

gous manner to access nucleosides related to dA and dI (see section

3.2.2).

By employing the nucleobase anion glycosylation under solid-

liquid conditions, a number of novel nucleosides as well as their 7-

substituted derivatives have been prepared, such as 7-deaza-2’-

deoxyguanosines 12a-h, 7-deaza-2’-deoxyadenosines 14a-e,g, 7-

deaza-2’-deoxyinosines 15a-e, 7-deaza-2’-deoxyxanthosines 35c,d,

2-amino-7-deaza-2’-deoxyadenosines 18a-f, 7-deaza-2’-

deoxyisoguanosines 36a-c, 36e, 7-deaza-2’-deoxyisoinosine (37),

2-halogenated 7-deaza-2’-deoxyadenosines 38a-e, 38i, and others

(Fig. 7).

3.2.1. Synthesis of 7-Deazapurine 2'-Deoxyribonucleosides Re-

lated to 2'-Deoxyguanosine and 2'-Deoxyxanthosine and Deriva-

tives Thereof (12b-h and 35c,d)

Using compound 28a as staring material, several nucleosides

functionalized at the 6-position were prepared by nucleophilic dis-

placement of the 6-chloro substituent. It has already been described

in Scheme 5 of section 3.1 that nucleoside 28a can be converted to

2-amino-2’-deoxytubercidin (18a) and 7-deaza-2’-deoxy-6-

thioguanosine (17). The 6-methoxy compound 11a was also pre-

pared from 28a (NaOMe in MeOH) (Scheme 9). The displacement

of the methoxy group of 11a by a hydroxyl function furnished 7-

deaza-2’-deoxyguanosine (12a) [34]. Here, an alkaline solution (0.2

M NaOH) was used for the conversion of OMe to the OH group,

which resulted in a fast and clean reaction.

Compound 11a is also a central intermediate for the synthesis

of 7-halogenated 7-deaza-2’-deoxyguanosines and halogenated 2’-

deoxyxanthosines. For this synthesis, 11a was converted to the fully

protected nucleoside 39a with N,N-dimethylformamide diethy-

lacetal followed by isobutyrylation (Scheme 10) [62]. Regioselec-

tive halogenation at position-7 was performed with N-

halosuccinimides (NXS, X = Cl, Br, and I) yielding the 7-

halogenated nucleosides 39b-d [63]. The 7-deazaguanosine analogs

N

N

Cl

H2NN

N NH

Cl

H2N

O

TolO

N

TolO

27a28a

TDA-1, KOH,

MeCN

70%

+ 7

N

N

Cl

N

N NH

Cl

O

TolO

N

TolO

33a

34a

TDA-1, KOH,

MeCN

81%

+ 7

Scheme 8.

HN

N

O

H2N

O

HO

N

HO

12a-h

N

N

NH2

O

HO

N

HO

14a-e,g

HN

N

O

O

HO

N

HO

15a-e

HN

NH

O

O

HO

N

HO

O

35c,d 36a-c,e

N

N

NH2

O

HO

N

HO

18a-f

H2N

HN

N

NH2

O

O

HO

N

HO

R R R R

R

R

a: R = H; b: R = Cl; c: R = Br; d: R = I; e: R = F; f: R = CN; g: R = NO2; h: R = CO2H

37

HN

NO

O

HO

N

HO

38i

N

NF

O

HO

N

HO

NH2

N

NCl

O

HO

N

HO

NH2 R

38a-e

Fig (7).


12b-d were accessible from 39b-d by methoxy/hydroxy substituent

exchange in refluxing 2 M NaOH [63]. Compounds 39b-d were

deprotected in 0.5 M NaOMe/MeOH to give 7-halogenated 4-

methoxy derivatives 11c,d. Deamination of compounds 11c,d with

NaNO2/AcOH yielded the derivatives 40c,d. Finally, the methoxy

group was displaced by a hydroxy group in 2 M NaOH under reflux

conditions (72 h), affording the 7-deaza-2’-deoxyxanthosines 35c,d

(Scheme 10) [64].

Treatment of the 7-iodo compound 12d with copper cyanide in

pyridine (method I) gave the 7-cyano derivative 12f in 86% yield

(Scheme 10) [65]. As these conditions require a long reaction time

(7 h) for the completion of the iodo-nitrile exchange, the conversion

was also performed under microwave conditions (method II) [66].

By applying method II, compound 12f was isolated in 59% yield

after 1 h. The 7-cyanonucleoside 39f was prepared from 39d in a

similar way, with (method I) and without (method II) microwave

assistance [65, 66]. Heating of 39f under mild alkaline conditions

(1.0 M NaOH at 60°C) provided 7-carbamoyl-7-deaza-2’-

deoxyguanosine (12j), while strong alkaline conditions (5 M KOH,

100°C) furnished 2’-deoxycadeguomycin (12h) (Scheme 11).

Also, 7-fluoro compounds were prepared. The synthesis of 7-

deaza-2’-deoxy-7-fluoroguanosine (12e) started from the 7-

fluorinated 7-deazapurine base 41e [67-69] (Scheme 12). The latter

was obtained from the 2-pivaloyl derivative 41a [70], which was

N

N

Cl

H2N

O

TolO

N

TolO

28a 12a

N

N

OMe

H2N

O

HO

N

HO

11a

NaOMe/MeOH,

reflux

88% 85%

0.2M NaOH,

reflux

HN

N

O

H2N

O

HO

N

HO

Scheme 9.

O

(i-Bu)O

N

N N

(i-Bu)O

OMe

HCHN

O

R

39b-d

O

(i-Bu)O

N

N N

(i-Bu)O

OMe

HCHN

O

39a

O

HO

N

N N

HO

OMe

H2N

O

HO

N

NH

N

HO

OMe

O

R R

c: 78%

d: 80%

c: 75%

d: 79%

R

O

HO

N

N N

HO

OMe

H2N

11a

NXS, DMF, rt

b: 71%

c: 78%

d: 92%

2M NaOH

reflux

b: 96%

c: 91%

d: 92%

NaOMe,

MeOH

AcOH/H2O,

NaNO2, rt

(i) Me2NHC(OEt)2, DMF

(ii) i-Bu2O, MeCN, rt

i: 90%

ii: 81%

39b-d 11c,d 35c,d40c,d

c: 87%

d: 65%O

HO

HN

NH

N

HO

O

O

R

O

HO

HN

N N

HO

O

H2N

R

12b-d

O

HO

HN

N N

HO

O

H2N

CN(I) CuCN, pyridine,

100°C, 7h

(II) CuCN, DMF,

130°C, 1h, MW

(I) 86%

(II) 59%

12f

a: R = H; b: R = Cl; c: R = Br; d: R = I

R

2M NaOH

Scheme 10.


fluorinated regioselectively at the 7-positon using Selectfluor in

MeCN in the presence of acetic acid. The glycosylation of 41e with

the sugar halide 7 (MeCN, KOH, TDA-1) furnished the protected

nucleoside 42e. Deprotection and displacement of the 6-chloro

group yielded the 6-methoxy compound 11e, which was trans-

formed afterwards with 2 N NaOH to the 2’-deoxyguanosine analog

12e [67-69]. The synthesis of 7-deaza-2’-deoxy-7-methylguanosine

(13) shown in Scheme 13 made use of the unprotected base 43

which was glycosylated ( 44) and transformed into 13 by a simi-

lar route as described for the 7-fluoronucleoside 12e [71].


lated to 2'-Deoxyadenosine and 2'-Deoxyinosine and Derivatives

Thereof (14a-g and 15a-e)

While the 7-deazaguanosine or 7-deazaxanthosine derivatives

were prepared from the nucleobase intermediates 27a and 41a, the

7-deazaadenosine analogs or 7-deazainosine derivatives were syn-

thesized employing 6-chloro-7-deazapurine (33a) and its 7-

substituted derivatives 33b-e (Scheme 14 and 15). Nucleobase an-

ion glycosylation of 33a-d [72] or 33e [73] with halogenose 7 per-

formed in MeCN in the presence of KOH and TDA-1 afforded the

O

(i-Bu)O

N

N N

(i-Bu)O

OMe

HCHN

O

I

39d

(I) CuCN, pyridine,

100°C, 7h

(II) CuCN, DMF,

130°C, 1h, MW

O

(i-Bu)O

N

N N

(i-Bu)O

OMe

HCHN

O

CN

39f

O

HO

HN

N N

HO

O

H2N

R

12h: R = COOH (57%)

j: R = CONH2 (47%)

12h: 5M KOH, 100°C, 1h

12j: 1M NaOH, 60°C, 15h

(I) 78%

(II) 58%

Scheme 11.

N

N NH

Cl

PivHN

41a

Selectfluor, MeCN,

AcOH, 50°C

30%

41e

N

N NH

Cl

PivHN

F

42e

N

N

Cl

PivHN

F

O

TolO

N

TolO

11e

N

N

OMe

H2N

F

O

HO

N

HO

NaOMe,

MeOH

87%

12e

HN

N

O

H2N

F

O

HO

N

HO

2N NaOH

70%

7, MeCN, KOH, TDA-1

64%

Scheme 12.

43

N

N NH

Cl

H2N

Me

44

N

N

Cl

H2N

Me

O

TolO

N

TolO

45

N

N

OMe

H2N

Me

O

HO

N

HO

NaOMe,

MeOH

84%

13

HN

N

O

H2N

Me

O

HO

N

HO

2N NaOH

80%

MeCN,

KOH, TDA-1

73%+

7

O

TolO

TolO

Cl

Scheme 13.


toluoyl-protected -D-nucleosides 34a-e in 65-81% yield (Scheme

14) [61, 67, 74, 75]. Compounds 34a-e were converted to the 2’-

deoxytubercidin derivatives 14a-e using conc. aq. ammonia at ele-

vated temperature (120°C) in a steel vessel (Scheme 15). The syn-

thesis of the corresponding 7-deaza-2’-deoxyinosine derivatives

15a-e used the same starting materials (34a-e). Sugar deprotection

in 0.5 M NaOMe in MeOH yielded the methoxy nucleosides 46a-e;

displacement of the methoxy group in 2 N NaOH furnished nucleo-

sides 15a-e [67, 76].

7-Deaza-2’-deoxyadenosine (14a) has been converted to its 7-

nitro derivative as shown in Scheme 16 [77-79]. For this purpose,

the amino group as well as the sugar hydroxy groups were protected

by acetylation (Ac2O/pyridine) yielding the intermediate 47. Nitra-

tion of 47 (HNO3/H2SO4 48) followed by deprotection

(NaOMe/MeOH) gave 7-deaza-2’-deoxy-7-nitroadenosine (14g). 7-

Deaza-7-nitropurine nucleosides, such as 14g and 7-deaza-2’-

deoxy-7-nitroguanosine (12g) have been utilized for DNA genotyp-

ing (Incorporation and Complete Chemical Cleavage, ICCC) [80]

and a footprinting technique (Template Directed Interference, TDI)

[81]. The synthesis of 12g was performed as described in section

3.2.4 (Scheme 29).

From 2’-deoxytubercidin (14a), the novel fluorescent and

chemically stable 1,N6-etheno-7-deaza-2'-deoxyadenosine 49 was

prepared by the reaction of 14a with 2-chloroacetaldehyde (Scheme

17) [82]. Compound 49 exhibits similar fluorescence properties as

its parent 1,N6-etheno-2'-deoxyadenosine. Its chemical stability

under acidic and alkaline conditions is significantly higher than that

of 1,N6-etheno-2'-deoxyadenosine. The use of 1,N

6-etheno-7-deaza-

2'-deoxyadenosine (49) is highly advantageous and superior to the

use of its purine congener, particularly for oligonucleotide synthe-

sis.

The solid-liquid nucleobase anion glycosylation was also ap-

plied to the synthesis of 7-deaza-2’-deoxy-2-fluoroadenosine (38i)

(Scheme 18). A reaction sequence starting with the fluorination of

the diamino nucleoside 18a under strongly acid conditions

(HF/pyridine) failed as the 2,6-diamino nucleoside 18a is unstable

under these conditions. Therefore, the corresponding nucleobase 50

was used, which was prepared from 2-amino-6-chloro-7-

deazapurine (27a) (see Scheme 8) by treatment with aq.

NH3/dioxane at 100°C in an autoclave. The diazotiza-

tion/fluorination reaction was performed in HF/pyridine by drop-

wise addition of tBuNO2 resulting in the 2-fluoro base 51 in 30%

yield. Glycosylation of 51 with halogenose 7 afforded the toluoyl-

protected -D-nucleoside 52 (74% yield). Compound 52 was depro-

tected in methanolic ammonia at room temperature to give 7-deaza-

2’-deoxy-2-fluoroadenosine (38i) [83].

In analogy to the 2-fluoronucleoside 38i, the 2-chloro com-

pound 38a and its 7-halogenated derivatives 38b-e were prepared

(Scheme 19). Glycosylation of 7-deaza-2,6-dichloropurine (53a)

[58] and its 7-halogenated derivatives 53b-e with sugar halide 7

(TDA-1/KOH/MeCN) furnished the intermediates 54a-e in 60-74%

O

TolO

N

N N

TolO

ClR

N

N NH

ClR

O

TolO

TolO

Cl

+

a: 81%

b: 70%

c: 75%

d: 65%

e: 67%

33a-e

734a-e

TDA-1, KOH,

MeCN, rt

a: R = H; b: R = Cl; c: R = Br; d: R = I; e: R = F

Scheme 14.

a: 70%

b: 75%

c: 86%

d: 70%

e: 89%

14a-e

O

HO

N

N N

HO

OMeR

46a-e

a: 90%

b: 90%

c: 90%

d: 95%

e: 85%


0.5M NaOMe,

MeOH, reflux

2N NaOH

reflux

a-d: aq. NH3,

dioxane, 120°C

e: NH3/MeOH

a: 75%

b: 75%

c: 79%

d: 80%

e: 83%

O

HO

N

N N

HO

NH2 R

O

HO

HN

N N

HO

OR

15a-e

34a-e

Scheme 15.

14a

Ac2O,

pyridine

97%O

AcO

N

N N

AcO

NHAc

47

O

AcO

N

N N

AcO

NHAc

48

HNO3/H2SO4 (1:1)

91%

NO2

O

HO

N

N N

HO

NH2 NO2

NaOMe,

MeOH

79%

14g

Scheme 16.


yield [84]. Selective displacement of the 6-chloro substituent by an

amino group (NH3/MeOH, 100°C) gave 2-chloro-7-deaza-2’-

deoxyadenosine (38a) or its 7-halogented derivatives 38b-e. The

photoreaction of 38a or 38e in diluted aq. NH3 yielded 7-deaza-2’-

deoxyisoguanosine (36a) or its 7-fluorinated derivative 36e [84,

85]. Compounds 54a-e were converted to the 6-methoxy derivatives

55a-e in NH3/MeOH at room temperature. In the case of 54a, com-

pound 55a (48%) was formed together with the 7-deaza-2,6-

dichloropurine 2’-deoxyribonucleoside 56 (30%). In a 0.5 M or

higher concentrated NaOMe/MeOH solutions and at elevated tem-

perature, both chloro substituents were displaced by methoxy

groups yielding the 2,6-dimethoxy derivatives 57a-e [84].

14a +

O

HCl

H2O

O

HO

N

N N

HO

N

H

Cl

O

HO

N

N N

HO

N

H

H

H

+

-Cl-

O

HO

N

N N

HO

49

N

-H+

Scheme 17.

N

N NH

NH2

H2N

N

N NH

NH2

F

N

N N

NH2

F

O

TolO

TolO

aq. NH3,

dioxane,

100°C

27a

50 51

52

91% 30% 74% 85%

38i

HF/pyridine,

tBuNO2, -50°C 7, TDA-1,

KOH, MeCN

NH3/MeOH,

rt

Scheme 18.

N

N NH

Cl

Cl

N

N N

Cl

Cl

O

TolO

TolO

53a-e

7, TDA-1,

KOH, MeCN

R

R

N

N N

NH2

Cl

O

HO

HO

38a-e

R

N

N N

OMe

Cl

O

HO

HO

55a-e

R

NH3,

MeOH,

100°C

NH3, MeOH, rt


N

N N

OMe

MeO

O

HO

HO

57a-e

R

a: 74%

b: 73%

c: 63%

d: 71%

e: 60%

a: 48%

b: 86%

c: 89%

d: 80%

a: 88%

b: 84%

c: 83%

d: 83%

a: 79%

b: 89%

c: 83%

d: 92%

0.5M NaOMe/MeOH, 60°C

HN

N N

NH2

O

O

HO

HO

36a,e

R

dilute aq. NH3,

hv

a: 54%

e: 35%

54a-e

N

N N

Cl

Cl

O

TolO

TolO

R

54a-e

Scheme 19.



lated to 2-Amino-2’-deoxyadenosine, 2'-Deoxyisoguanosine, 2'-

Deoxyisoinosine, and Derivatives Thereof (18a-e, 36a-c and 37)

Compound 28a was transformed to the 2,6-diamino 7-

deazapurine nucleoside 18a (Scheme 20). The selective deamina-

tion of 18a at position-2 with NaNO2/AcOH/H2O furnished 7-

deaza-2’-deoxyisoguanosine (36a) [86].

The syntheses of the 7-halogenated 2-amino-7-deazaadenine

nucleosides 18b-d and 7-deaza-2’-deoxyisoguanine derivatives

36b,c were carried out according to Scheme 21 [70, 87, 88]. As

direct halogenation of 2-amino-6-chloro-7-deazapurine (27a) takes

place at the 8-position, the 2-amino group of 27a was protected

with a pivaloyl residue giving the 2-pivaloyl derivative 41a. The

halogenation reactions of 41a with N-halosuccinimides (NXS, X =

Cl, Br, and I) were performed in CH2Cl2 yielding 7-halogenated

compounds 41b-d exclusively [70, 87, 88]. Subsequent solid-liquid

nucleobase anion glycosylations of 41b-d with halogenose 7 (TDA-

1/KOH/MeCN) afforded the toluoyl-protected nucleosides 42b-d in

62-68% yield (Scheme 21) [70, 88]. Removal of the toluoyl protect-

ing groups and displacement of the 6-chloro substituents of 42b-d

were performed in 25% aq. ammonia in a steel bomb. The 2,6-

diamino nucleosides 18b-d were formed, and the 7-halogen sub-

stituents were not displaced under these conditions. Selective

deamination of 18b or 18c with sodium nitrite in AcOH/H2O (V/V,

1:5) furnished 7-chloro-7-deaza-2'-deoxyisoguanosine (36b) and

the corresponding 7-bromo derivative 36c.

When the deprotection/displacement conditions used for the

conversion of 42b-d were applied to the corresponding 7-

fluorinated derivative 42e, decomposition of the molecule was ob-

served [84]. Under more moderate reaction conditions (NH3,

MeOH, 70°C, 5 d), the diamino compound 18e (33%) was formed

together with 29e (26%) and 11e (21%) as by-products (Scheme

22). Efforts to convert 18e into 7-deaza-2’-deoxy-7-fluoroiso-

guanosine (36e) by deamination conditions which were employed

for the other halogenated derivatives 18b-d led to the decomposi-

tion of 18e. Instead, nucleoside 36e was obtained from 38e by pho-

tochemical conversion as shown in Scheme 19 (see section 3.2.2).

Isoguanosine (iG) as well as its 2'-deoxyribonucleoside (iGd)

form a significant proportion of enol tautomers in aqueous solution

(10%). They are responsible for non-selective base recognition

during hybridization, which finally results in mutagenicity [89-91].

The replacement of iGd by 7-deaza-2'-deoxyisoguanosine (36a)

increases the content of the keto tautomer significantly with KTAUT

= [keto]/[enol] = 1000 [92]. The introduction of 7-halogen substitu-

ents shifts the tautomeric keto-enol equilibrium of 36b and 36c

further towards the keto form with KTAUT [keto]/[enol] 104 com-

ing close to that of 2’-deoxyguanosine (104

105) [93] (Fig. 8). As a

result, nucleosides 36b and 36c show a much better mismatch dis-

crimination against dT than iGd in antiparallel as well as in parallel

DNA [93]. Therefore, they can be expected to increase selectivity

of base incorporation opposite to isoCd in the polymerase-catalyzed

elongation of triphosphates reaction.

N

N

Cl

H2N

O

TolO

N

TolO

N

N

NH2

H2N

O

HO

N

HO

18a

HN

N

NH2

O

O

HO

N

HO

36a

aq. NH3,

dioxane

AcOH/H2O,

NaNO2, rt

88% 67%

28a

Scheme 20.

N

N NH

Cl

PivHN

27a 41a 41b-d

N

N NH

Cl

H2N

t-BuCOCl,

pyridine NXS, CH2Cl2

84% b: 81%

c: 80%

d: 85%

7, MeCN,

KOH, TDA-1

42b-d

HN

N

NH2

O

R

aq. NH3/dioxane,

120°C, 24h

.

b: 85%

c: 88%

d: 89%

AcOH/H2O,

NaNO2, rt, 0.5h

N

N NH

Cl

PivHN

R

N

N

Cl

PivHN

R

O

TolO

N

TolO

O

HO

N

HO

N

N

NH2

H2N

R

O

HO

N

HO

18b-d 36b,c

b: R = Cl; c: R = Br; d: R = I

b: 62%

c: 68%

d: 58%

b: 61%

c: 65%

Scheme 21.


a: R = H; b: R =Cl; c: R = Br

KTAUT

HN

N

NH2

OHO

HO

NO

N

N

NH2

OHO

HO

NHO

36a-c (keto) 36a-c (enol)

36a: K TAUT = 103

36b: KTAUT = 104

36c: KTAUT = 104

R R

Fig (8). Tautomeric equilibrium of 7-deaza-2’-deoxyisoguanosines 36a-c.

Single-crystal X-ray analysis of 7-deaza-2’-deoxyisoguanosine

(36a) and its 7-bromo derivative 36c confirms that both nucleosides

form the N1-H, 2-keto-6-amino tautomer in the crystalline state [93,

94] (Fig. 9). The sugar ring adopts a C2’-endo sugar conformation

with S-type pucker in both crystals. The predominant conformation

in aqueous solution is also S [70].

7-Deaza-2’-deoxyisoinosine (37), which is the 6-deamino ana-

log of 2'-deoxyisoguanosine, is a highly fluorescent nucleoside with

a quantum yield of 0.22 [95]. It was synthesized utilizing 6-chloro-

7-deaza-2-methoxypurine (58) as a starting material [96] (Scheme

23). Glycosylation of 58 with halogenose 7 under solid-liquid con-

ditions (KOH, TDA-1, MeCN) yielded 59 [97]. Catalytic hydro-

genation of the latter furnished the protected 2-methoxy compound

60, which was deblocked (NH3/MeOH) to give nucleoside 61. The

latter was treated with 2 N NaOH in the presence of DMSO under

reflux conditions furnishing nucleoside 37. The fluorescence spec-

trum of 37 is shown in Fig (10). Compound 37 shows an emission

maximum at 440 nm upon excitation at 328 nm [98].

3.2.4. Nucleobase Anion Glycosylation - Sodium Salt Procedure

The sodium salt procedure generates 7-deazapurine anions with

sodium hydride. It goes back to a protocol developed by Goto for

the ribonucleoside Q synthesis in 1977 [35, 36]. As 2,3,5-tri-O-

benzyl-D-ribofuranosyl bromide, which was used for the glycosyla-

tion, exists as an anomeric mixture and the benzyl groups do not

assist in neighboring group participation from the -side, the out-

come of this glycosylation reaction is an anomeric mixture of -

and -nucleosides. Later, a number of 7-deazapurine -D-

arabinonucleosides were prepared in our laboratory by this tech-

nique [37, 54, 99]. In 1984, Robins and Kazimierczuk used NaH to

generate the nucleobase anion with MeCN as solvent and employed

the sugar halide 7 in the glycosylation reaction [38]. This method

was applied to the synthesis of a number of 7-dezapurine 2'-

deoxyribonucleosides, such as 7-deaza-2’-deoxyguanosine (12a),

its derivatives 12d, 12g, 12h, 12j [100-103], and related 2’-

deoxytubercidin derivatives 14a, 14f, 14j, 18f, 21, 38a, and 62-68

(Fig. 11) [38, 39, 104-106].

42e

N

N

Cl

PivHN

F

O

TolO

N

TolO

N

N

NH2

H2N

F

O

HO

N

HO

18e (33%)

N

N

Cl

H2N

F

O

HO

N

HO

29e (26%)

N

N

OMe

H2N

F

O

HO

N

HO

11e (21%)

NH3, MeOH

70°C, 5d+ +

Scheme 22.

(A)

(B)

Fig (9). Perspective views showing the displacement ellipsoids obtained from the single-crystal X-ray analyses of compounds 36a (A) and 36c (B).


The synthesis of the 2-substituted 2’-deoxytubercidin deriva-

tives 38a and 21 by the sodium salt protocol is shown in Scheme 24

[38]. The nucleobase anion of 53a or 69 [107] which was generated

with NaH, was glycosylated with the halogenose 7 yielding -D-

nucleosides 54a or 70. They were deprotected and aminated at posi-

tion-6 to give compounds 38a or 21 (aq. NH3, 110°C).

Our laboratory used the sodium salt protocol for the synthesis

of 7-deaza-2’-deoxyxanthosine (35a). The glycosylation of 7-

deaza-2,6-dichloropurine (53a) with 7 was performed in DMF in

the presence of NaH yielding the -D-nucleoside 54a (53%)

(Scheme 25). The latter was transformed to 2,6-dimethoxy nucleo-

side 57a. Demethylation of 57a with 33% HBr/AcOH furnished the

xanthosine derivative 35a [108].

In the crystalline state, compound 35a forms water-filled nano-

tubes with C-H· · · O hydrogen bonds (Fig. 12A and Fig. 12B)

[109]. In addition to the intermolecular hydrogen bonds (N3-H· · ·

OH-5’), an array of further hydrogen bonds stabilizes a su-

pramolecular aggregate of four molecules of 35a. These interac-

tions cause the formation of an almost flat tetramer (Fig. 12A) with

an oval cavity at the center that has the approximate dimensions of

9.5 6.5 3.0 Å3 (± 0.5 Å

3). A pile of completely stacked tetramers

forms a nanotube-like structure (Fig. 12B). Compound 35a repre-

58

N

N NH

Cl

MeO

MeCN, KOH, TDA-1

59

NH3,

MeOH

N

N

Cl

MeO

O

TolO

N

TolO

60

N

NMeO

O

TolO

N

TolO

Pd/C, H2

61

N

NMeO

O

HO

N

HO

HN

NO

O

HO

N

HO

2N NaOH,

DMSO

+ 7

37

86% 92%

81% 85%

Scheme 23.

Fig (10). Fluorescence spectra of nucleoside 37 in water. The concentration of 37 was 10-5

M.

HN

NO

O

HO

N

HO

37


sents a new nanostructure which binds water molecules inside a

nanotube.

The sodium salt glycosylation was also applied to the synthesis

of 2’-deoxytoyocamycin (14f) and 2’-deoxysangivamycin (14j)

using 2-amino-5-bromopyrrol-3,4-dicarbonitrile (71) as starting

material (Scheme 26). After protection of the amino group with

diethoxymethyl acetate in MeCN, compound 71 was glycosylated

with halogenose 7 in the presence of NaH yielding the intermediate

72. This was cyclized in NH3/MeOH to give 8-bromo-7-cyano-7-

deaza-2’-deoxyadenosine (73). 2’-Deoxytoyocamycin (14f) was

prepared from 73 by a three step procedure (acetylation, debromi-

nation, and deacetylation) [104, 106]. Then, compound 14f was

converted to 2’-deoxysangivamycin (14j) using H2O2/NH3·H2O

[104].

Similarly, 7-cyano-7-deaza-2,6-diaminopurine 2’-deoxyribo-

nucleoside (18f) was prepared [87] using 7-cyano-7-deaza-2,6-

diaminopurine (77) as starting material (Scheme 27). Nucleobase

77 was synthesized from 71 by debromination (H2/Pd/BaCO3,

76), followed by ring-closure with chloroformamidine hydrochlo-

ride at 170°C. In order to increase solubility, compound 77 was

transformed to the more soluble 78. Glycosylation of 78 with halo-

genose 7 (NaH/MeCN) gave -D-nucleoside 79, which was depro-

tected using aq. NaOH/pyridine/MeOH ( 80) followed by 40%

aq. MeNH2 resulting in nucleoside 18f.

N

N

NH2

O

HO

N

HO

R

N

N

NH2

O

HO

N

HO

RN

N

NH2

O

HO

N

HO

R

38a: R = Cl

21: R = SCH3

62: R = CH3

63: R = CH3

64: R = Cl

N

N

O

HO

N

HO

CH3

65

N

N

O

O

HO

N

HO

R

H2N

12a: R = H

d: R = I

g: R = NO2

h: R = CO2H

j: R = CONH2

14a: R = H

f: R = CN

j: R = CONH2

N

N

O

HO

N

HO

CH3

66

N

N

O

HO

N

HO

68

H3CS

S

N

N

NH2

O

HO

N

HO

H2N

18f

CN

N

N

NH2

O

HO

N

HO

Cl

H3C

67

H

Fig (11).

54a

68%

N

N

OMe

MeO

O

HO

N

HO

57a

HN

NH

O

O

HO

N

HO

35a

60%

NaOMe, MeOH O HBr, AcOH

53a + 7NaH, DMF

53%

Scheme 25.

O

TolO

N

N N

TolO

Cl

N

N NH

Cl

O

TolO

TolO

Cl

+ NaH, MeCN

53a: R = Cl

69: R = SCH3

7

NH3/H2O,

110°C

O

HO

N

N N

HO

NH2

R

R R

54a: 60%

70: 66%

38a: 61%

21: 72%

54a: R = Cl

70: R = SCH3

38a: R = Cl

21: R = SCH3

Scheme 24.


(A) (B)

Fig (12). Crystalline nanotubes of stacked tetramers of 7-deaza-2’-deoxyxanthosine (35a) units.

O

TolO

TolOO

TolO

TolO

Cl

+

71

772

O

HO

N

N N

HO

NH2

73

NH

NC

H2N

CN

Br

N

NC

N

CN

Br

EtO

CN

Br

NH3/MeOH, rt

(i) diethoxymethylacetate,

MeCN, reflux

(ii) NaH, MeCN

75% 77%

O

AcO

N

N N

AcO

NH2

74

CN

Br

O

AcO

N

N N

AcO

NH2 CN

O

HO

N

N N

HO

NH2 R

Ac2O,

pyridine

BSA, MeCN, KF,

18-crown-6 ether NH3/MeOH

97% 56% 10%

7514f: R = CN

j: R = CONH2

H2O2/aq. NH3

BSA = N,O-bis(trimethylsilyl)acetamide

Scheme 26.

7, NaH,

MeCN

H2/Pd/BaCO3,

DMF/MeOH

NH

NC

H2N

CN

NH2

ClH2N

Cl

Dowtherm A,

170°C, 80%

N

N NH

NH2 CN

H2N

N

N NH

NHPivCN

PivHN

O

TolO

N

N N

TolO

NHPivCN

PivHN

O

HO

N

N N

HO

NH2 CN

H2N

40% aq. MeNH2,

55°C, 18h

pivaloyl chloride,

pyridine

60% 72%

70%

71

76 77 78

79 18f

O

HO

N

N N

HO

NHPivCN

PivHN

80

aq. NaOH,

pyridine, MeOH

96%

Scheme 27.


7, NaH, MeCN

74%

28f

N

N

Cl

H2N

CN

O

TolO

N

TolO

12h

HN

N

O

H2N

CO2H

O

HO

N

HO

64%

HN

N

O

H2N

C

NH

HN

N

O

H2N NH2

OMe

O

Cl

CHO

HN

N

O

H2N N

OMe

O

OCMe3O

NH2

O

N

N

Cl

H2N

CN

NH

+ HN

N

O

H2N NH

OMe

O

50%

DBDC,

DMF-TEA

50%

NH3/MeOH,

120°C

73%

POCl3,

DEA

40%

12j

HN

N

O

H2N

C

O

HO

N

HO

NH3/MeOH

88%

29f

N

N

Cl

H2N

CN

O

HO

N

HO

NH2

O

NaOAc,

100°C

H2O2,

NH3/H2O

56%

81 82 83 84

85 27f

5M KOH

Scheme 28.

The synthesis of 2’-deoxycadeguomycin (12h) by the sodium

salt procedure is shown in Scheme 28 [101, 110]. The condensation

of 81 with 82 was performed in aq. NaOAc solution to give the 7-

deazaguanine derivative 83. After protection of the pyrrole nitrogen

with a t-BOC group ( 84), the methyl ester was converted to an

amide with concomitant deprotection of the t-BOC group yielding

nucleobase 85. Chlorination with POCl3 in the presence of N,N-

diethylaniline (DEA) gave 6-chloro-7-cyano-7-deazapurine (27f).

Glycosylation of 27f with halogenose 7 (NaH/MeCN) furnished the

protected nucleoside 28f. Deprotection of 28f yielded compound

29f, which was converted to 7-carbamoyl-7-deaza-2’-

deoxyguanosine (12j) using H2O2/NH3/H2O. The amide hydrolysis

of 12j with 5 M KOH afforded 2’-deoxycadeguomycin (12h).

The sodium salt procedure was also applied to the synthesis of

7-deaza-2’-deoxy-7-nitroguanosine (12g) (Scheme 29). The nitro

group was introduced in 41a (see Scheme 21) with HNO3/H2SO4

(1:1) yielding the 7-nitro derivative 41g, which was converted to 7-

nitro-7-deazapurine 9g. Compound 9g was glycosylated with 2-

deoxy-3,5-di-O-(p-chlorobenzoyl)- -D-erythro-pentofuranosyl

chloride (86) in DMF in the presence of NaH resulting in -D-

nucleoside 87. Demethylation (Me3SiCl/NaI/MeCN, 88) was

followed by deprotection with K2CO3/MeOH, yielding 7-deaza-2’-

deoxy-7-nitroguanosine (12g) [78, 79].

3.3. 7-Deazapurine 2’-Deoxyribonucleosides From Ribonucleo-

sides by Deoxygenation

As mentioned in the introduction of section 3, chemical deoxy-

genation of ribonucleosides to their corresponding 2’-

deoxyribonucleosides offers an expedient route when other syn-

thetic or enzymatic protocols fail. Different deoxygenation proce-

dures were applied to purine or pyrimidine ribonucleosides with

variable success [111-113].

7-Deazapurine ribonucleoside 2’-deoxyribonucleoside con-

version is reported in an early publication (1976) of Robins and

Muhs, in which the transformation of the antibiotic tubercidin (89a)

to its 2’-deoxyribo derivative (14a) is described [114]. The reaction

sequence includes hydroxyl and amino group protection, introduc-

tion of a mesyloxy group followed by catalytic hydrogenation to

yield eventually the deoxygenated target compound 2’-

deoxytubercidin (14a) in 27% overall yield over eight steps

(Scheme 30).

In the mid 1970s, Barton and McCombie developed a versatile

method for the deoxygenation of alcohols by radical reduction

[115]. This protocol comprises the conversion of the respective

alcohol to a thiocarbonyloxy derivative as a first step. Second, the

thiocarbonyl oxy derivative is treated with tri-n-butyltin hydride (n-

Bu3SnH) together with a radical initiator to finally yield the deoxy-

genated compound by a radical-mediated mechanism.

Later, Robins and Wilson made use of the Barton-McCombie

deoxygenation to establish a four-step procedure for the specific

conversion of ribonucleosides to their corresponding 2’-

deoxyribonucleosides [116]. This protocol was also applied for the

conversion of tubercidin (89a) and toyocamycin (89f) into the cor-

responding 2’-deoxyribonucleosides 14a,f,j as shown in Scheme 31

[117]. First, the respective ribonucleoside 89a or 89f was treated

with Markiewicz’s reagent (1,3-dichloro-1,1,3,3-tetraisopropyl-


NaH, DMF, 0°C

61%

87

N

N

OMe

H2N

NO2

O

pCl BzO

N

pCl BzO

88

HN

N

O

H2N

NO2

O

pCl BzO

N

pCl BzO

12g

HN

N

O

H2N

NO2

O

HO

N

HO

79%

Me3SiCl,

NaI, MeCN

73%

86

O

pCl BzO

pCl BzOCl

41a

41g

N

N NH

Cl

PivHN

NO2

9g

N

N NH

OMe

H2N

NO2

HNO3/H2SO4

78%

NaOMe,

MeOH

65%

K2CO3, MeOH

Scheme 29.

N

N

NH2

O

HO

N

HO

14a

N

N

NH2

O

N

HO

90

N

N

NBz2

O

N

BzO

N

N

NHBz

O

N

BzO SBn

O O

OH

N

N

NH2

O

HO

N

HO

89a

OH

N

N

NHBz

O

N

HO SBn

OH

N

N

NHBz

O

N

BzO SBn

OMs

+

91

92a (68%) 92b (22%) 93

N

N

NH2

O

N

HO SBn

OH

94

N

N

NH2

O

N

HO BnS

95

benzoylation

sodium benzylthiolate,

hot THF

quantitatively

92a: mesylation

1) Na benzoate, hot DMF

2) NaOMe, MeOH

HO

+

95: Ra-Ni,

DMF, 100°C

77%

Scheme 30.


O

HO

HO

89a,f

OH

O

O

O

96a,f

OH

Si

O

Si

i-Pr i-Pr

i-Pr

i-Pr

(i-Pr)2ClSiOSi(i-Pr)2Cl,

pyridine, rt

O

O

O

OCOPh

Si

O

Si

i-Pr i-Pr

i-Pr

i-Pr

S

PhOC(S)Cl, DMAP,

MeCN, rt

O

O

O

98a,f

Si

O

Si

i-Pr i-Pr

i-Pr

i-Pr

(n-Bu)3SnH, AIBN,

toluene, 75°C 1M TBAF/THF

N

NN

NH2

N

N N

NH2

N

NN

NH2

N

N N

NH2

R

97a,f

97a,f

R R

R

O

HO

HO

14a: 68% overall yield

f: 69% overall yield

N

N N

NH2 R

14f: Dowex 1-X2 (OH-)

14j (65% overall yield)

a: R = H; f: R = CN

O

HO

HO

N

N N

NH2 CONH2

Scheme 31.

disiloxane) [118] to simultaneously protect the 3’- and 5’-hydroxyl

groups of the sugar moiety ( 96a,f). Reaction of the silylated

nucleoside 96a,f with phenoxythiocarbonyl chloride in the presence

of dimethylaminopyridine (DMAP) using acetonitrile as solvent

gave the 2’-O-phenoxythiocarbonyl derivative 97a or 97f. Reduc-

tive deoxygenation of 97a or 97f was performed with tri-n-

butyltin(IV) hydride in toluene at 75°C using , ’-

azoisobutyronitrile (AIBN) as radical initiator and furnished the

silylated nucleosides 98a,f. The last step comprised desilylation

with tetra-n-butylammonium fluoride (TBAF) in THF to give the

free 2’-deoxyribonucleoside 14a or 14f. 2’-Deoxytubercidin (14a)

and 2’-deoxytoyocamycin (14f) were obtained in 68% and 69%

yield, respectively which is superior to any other chemical trans-

formation protocol employing the corresponding parent ribonucleo-

sides as precursors [117]. 2’-Deoxytoyocamycin (14f) was further

converted to 2’-deoxysangivamycin (14j; 65% overall yield over 5

steps) by passing an aqueous solution of 14f through a column of

Dowex 1-X2 (OH-) resin (Scheme 31).

Depending on the structure of the target nucleosides, variations

of the Barton-McCombie deoxygenation were used to synthesize

2’- and 3’-deoxyribonucleosides as well as 2’-3’-dideoxyribo-

nucleosides (see also section 4.3) [119-123].

4. FUNCTIONALIZATION OF 7-DEAZAPURINE 2'-

DEOXYRIBONUCLEOSIDES

4.1. Alkynylated 7-Deazapurine Nucleosides Prepared by the

Palladium-catalyzed Sonogashira Cross Coupling Reaction

The introduction of alkynyl- or aminoalkynyl side chains into

7-deazapurine nucleosides has a major impact on the duplex stabil-

ity when these compounds are constituents of duplex DNA or RNA

[87, 100, 124-126]. Furthermore, oligonucleotides become resistant

against enzymatic degradation [127]. Nucleosides, nucleotides or

oligonucleotides with aminoalkynyl chains are used for the func-

tionalization with reporter groups applied to nucleic acid sequenc-

ing or as tools in DNA or RNA diagnostics [128-134]. More re-

cently, 7-deazapurine 2’-deoxyribonucleosides carrying a terminal

triple bond within their side chain have been used as precursors in

the copper(I)-catalyzed Huisgen-Meldal-Sharpless alkyne-azide

cycloaddition (“click” reaction) (for more details see section 4.1.1)

[135-137]. The 7-iodo derivatives of 7-deazapurine 2’-

deoxyribonucleosides described in section 3.2 were employed as

starting materials for the introduction of alkynyl or aminoalkynyl

chains by the Pd-catalyzed Sonogashira cross-coupling reaction

[75]. Exemplified cross-coupling reactions performed on the iodo

nucleosides 12d, 14d, 18d, and 15d are depicted in Scheme 32.

The cross coupling reactions of 7-deaza-7-iodopurine 2’-

deoxyribonucleosides 12d, 14d, 15d, and 18d with the correspond-

ing alkynes were performed in anhydrous DMF in the presence of

tetrakis(triphenylphosphine)palladium(0) [Pd(0)(PPh3)4], copper(I)

iodide, and triethylamine under argon atmosphere, yielding the 7-

alkynyl- or aminoalkynyl derivatives 99a,b,d,f,h-k [63, 100, 126,

138-141], 100a-i,k [75, 100, 124, 142-144], 101b,i [87, 126], or

102f,g,i [126, 145, 146] (Scheme 32). This protocol was also em-

ployed for the construction of steroid-nucleoside conjugates (103,

104), employing 17 -ethynylestradiol or 17 -ethynyltestosterone

(Fig. 13) [75]. Some of the above mentioned nucleosides were

transformed to the corresponding phosphoramidites 105a,b,f [141,

144, 147], 106b,d,h-k [127, 138, 140, 144, 147], 107a,d,g,h [124,

142], 108b,f,i,k [139, 144, 148, 149], and 109f,g,i [126, 145, 146],

which were used in solid-phase oligonucleotide synthesis (Fig. 14).

Sonogashira cross coupling reactions were also performed in

aqueous medium (H2O/MeCN) using Pd(OAc)2 as catalyst and

3,3 ,3 -phosphinidyne tris(benzenesulfonic acid) trisodium salt

(P(PhSO3Na)3; TPPTS) as water soluble ligand in the presence of


12d

O

HO

HN

N N

HO

O

H2N

O

HO

HN

N N

HO

O

H2N

I R

100a-i,k

O

HO

N

N N

HO

NH2 R

(CH2)4

a: R =

b: R =

c: R =

d: R =

e: R =

f: R =

CH3

(CH2)3CH3

99a,b,d,f,h-k

NPhthCH2

(CH2)3NHCOCF3

(CH2)2CH3

CH2NHCOCF3g: R =

h: R =

i: R =

j: R =

k: R =

101b,i

O

HO

N

N N

HO

NH2 R

H2N

Pd(0)(PPh3)4, CuI,

Et3N, DMF, R-H

14d

O

HO

N

N N

HO

NH2 I

18d

O

HO

N

N N

HO

NH2 I

H2N

Pd(0)(PPh3)4, CuI,

Et3N, DMF, R-H

Pd(0)(PPh3)4, CuI,

Et3N, DMF, R-H

102f,g,i

O

HO

HN

N N

HO

OR

15d

O

HO

HN

N N

HO

OI

Pd(0)(PPh3)4, CuI,

Et3N, DMF, R-H

(CH2)4CH3

NPhth(CH2)2

N

H

Scheme 32.


O

HO

N

N N

HO

NH2

103

C

HO

C

CH3

O

CH3

O

HO

N

N N

HO

NH2 C

HO

C

OH

CH3

104

Fig (13).

PN(i-Pr)2NCCH2CH2O

O

O

N

N N

DMTO

R1

PN(i-Pr)2NCCH2CH2O

O

O

HN

N N

DMTO

O

N

R R

105a,b,f 107a,d,g,h

PN(i-Pr)2NCCH2CH2O

O

O

N

N N

DMTO

NMe2NHC R

(CH2)4a: R =

b: R =

d: R =

CH3

(CH2)3CH3

NPhthCH2

(CH2)3NHCOCF3

CH2NHCOCF3

f: R =

g: R =

h: R =

NPhth(CH2)2

N

Me2NHC

PN(i-Pr)2NCCH2CH2O

O

O

HN

N N

DMTO

O

(i-Bu)HN

R

106b,d,h-k 108b: R1 = N=C(Me)NMe2

f: R1 = NH(i-Bu)

i: R1 = NHAc

k: R1 = NH(i-Bu)

PN(i-Pr)2NCCH2CH2O

O

O

HN

N N

DMTO

OR

109f,g,i

i: R =

j: R =

k: R =

Fig (14).

CuI and Et3N. Due to the aqueous conditions, nucleoside triphos-

phates can also be employed in the cross coupling reaction. 7-

Deaza-2’-deoxy-7-iodoadenosine (14d) or its triphosphate analog

110 were utilized as precursors together with the respective alkynes

to synthesize various nucleoside or nucleoside triphosphate conju-

gates with bipyridine ligands (111a,b), ruthenium bipyridine com-

plexes (111c,d, 112d), ferrocene (112e), amino acids (111f, 112f)

or bile acids (111g, 112g) attached to position-7 of the nucleobase

(see Scheme 33 for selected examples) [150-154]. Alternatively, the

aqueous-phase Suzuki-Miyaura cross coupling reaction was applied

to introduce similar reporter groups into position-7 of the 7-

deazapurine moiety as shown in Scheme 34. Reactions of the corre-

sponding boronate precursors 113a-c or 114d-i with iodo nucleo-

side 14d or iodo nucleotide 110 in the presence of Pd(OAc)2-

TPPTS and Cs2CO3 in MeCN/H2O afforded the 7-substituted com-

pounds 115a-g [153, 154] as well as 116g-i [153, 155, 156]. Nu-

cleoside triphosphate conjugates 112d-g and 116g-i obtained by

either of the above mentioned coupling reactions have been suc-

cessfully subjected to enzymatic incorporation into oligonucleotides

[150-153, 155, 156].

Single-crystal X-ray analyses of 7-deaza-2’-deoxy-7-propynyl-

guanosine (99b) and 7-deaza-2’-deoxy-7-propynyladenosine (100b)

were reported by our laboratory [157, 158] (Fig. 15). In both com-

pounds, the orientation of the nucleobase relative to the sugar moi-

ety is anti with the torsion angle (O4’-C1’-N9-C4) of -117.1 (5)°

for 99b and of -130.7 (2)° for 100b. The sugar moieties of these

nucleosides adopt the S-conformation (99b: P = 152.5° with an

amplitude m = 41.9°; 100b: P = 185.9°, m = 39.1°). The linear

propynyl group is inclined by 4.6° to the nucleobase for 99b and by

1.6° for 100b. The triple bond length is 1.184 (7) Å for 99b and

1.185 (3) Å for 100b, which is in the range of non-conjugated tri-

ple-bonds.

In the multi-layered network of nucleoside 99b, the nucleobases

are stacked head-to-head with the closest distance of 3.728 (1) Å.

This is slightly higher than the average base pair stacking distance

in B-DNA (3.5 Å) (Fig. 16A). In contrast, a head-to-tail stacking of


O

HO

N

N N

R2O

NH2

14d: R = H

O

HO

N

N N

RO

NH2 I

111a: R1 = a, R2 = H

111b: R1 = b, R2 = H

111c: R1 = c, R2 = H

111d: R1 = d, R2 = H

112d: R1 = d, R2 = P3O104 -

112e: R1 = e, R2 = P3O104 -

111f: R1 = f, R2 = H

112f: R1 = f, R2 = P3O104 -

111g: R1 = g, R2 = H

112g: R1 = g, R2 = P3O104 -

R1

N N N N

N N

RuII(bpy)2

2 PF6-

N N

RuII(bpy)2

2 PF6-

Fe

Pd(OAc)2, TPPTS, Et3N,

CuI, DMF or H2O/MeCN

a b c

d

e

NH2

COOH

f

R1 =

HO

OH

O

O

OHH

g

R1

P O

O

O

P O

O

O

P

O

O

O110: R =

Scheme 33.

O

HO

N

N N

R2O

NH2

14d: R = H

O

HO

N

N N

RO

NH2 I

115a: R1 = a, R2 = H

115b: R1 = b, R2 = H

115c: R1 = c, R2 = H

115d: R1 = d, R2 = H

115e: R1 = e, R2 = H

115f: R1 = f, R2 = H

115g: R1 = g, R2 = H

116g: R1 = g, R2 = P3O104 -

116h: R1 = h, R2 = P3O104 -

116i: R1 = i, R2 = P3O104 -

N N

N N

RuII(bpy)2

2 PF6-

Pd(OAc)2, TPPTS, Cs2CO3

or Na2CO3, H2O/MeCN

a

d

NH2

COOH

g

R1 =

NNN

N

N

RuII(bpy)2

2 PF6-

RuII(tpy)

2 PF6-

N N N

N

N

NH2 NO2

R1

R1 B

O

O

113a-c

R1 B

OH

OH

114d-i

b c

e f

h i

113a-c or 114d-i,

P

O

O

O P

O

O

O P

O

O

O

110: R =

Scheme 34.


(A) (B)

Fig (15). Perspective views of (A) 7-deaza-2’-deoxy-7-propynylguanosine (99b) and (B) 7-deaza-2’-deoxy-7-propynyladenosine (100b). Displacement ellip-

soids are drawn at the 50% probability level.

(A) (B)

Fig (16). Views showing (A) head-to-head base stacking of nucleoside 99b and (B) head-to-tail base stacking of nucleoside 100b.

nucleoside nucleoside"click" reaction

reporter groupreporter groupN3

N N

N

Fig (17). Schematic illustration of the “click” reaction.

nucleobases is observed for nucleoside 100b (Fig. 16B). The closest

distance of the stacked bases is 3.197 (1) Å for 100b, which is

smaller than the average base pair stacking distance in B-DNA.

4.1.1. Functionalization of 7-Deazapurine 2’-Deoxyribonucleo-

sides Empolying the “Click” Reaction

The copper(I)-catalyzed Huisgen-Meldal-Sharpless 1,3-dipolar

cycloaddition of organic azides and alkynes (“click” reaction,

CuAAC reaction) has emerged as one of the ideal bio-orthogonal

protocols for the preparation of rich chemical diversity [159-161].

This cycloaddition is driven by the high energy content of the com-

ponents (azides and alkynes), yielding less reactive 1,2,3-triazoles,

which are highly stable to oxygen, light, and aqueous environment

[159, 160]. In nucleic acid chemistry, the CuAAC reaction has been

performed on nucleoside, nucleotide as well as on oligonucleotide

level in solution, on solid support, or on surfaces [for e.g. see 137,

162-177].

The synthesis of azide-modified DNA is encountered with dif-

ficulties. As azides are prone to reduction during solid-phase oli-

gonucleotide synthesis, the alkyne component is usually attached to

the nucleoside, while the reporter group carries the azido function-

ality. To avoid perturbation of the DNA structure, the “click” reac-

tion is performed most efficiently when the ligand is introduced in

the major groove of DNA. In this regard, position-7 of 7-

deazapurine 2’-deoxyribonucleosides - as purine surrogates - has

become an ideal site for introducing side chains with terminal triple


bonds [87, 100, 124-126]. The alkynylated nucleosides 99a,f,

100a,f and 102f employed in “click” reactions are shown in section

4.1, Scheme 32. As ligands, simple residues such as benzylazide

(117) [178, 179] as well as fluorescent or fluorogenic reporter

groups have been used (Fig. 18), affording highly fluorescent nu-

cleosides. Fig. (17) schematically outlines the “click” reaction em-

ploying benzylazide 117, 3-azido-7-hydroxycoumarin 118, 3-azido-

7-methoxycoumarin 119, 1-azidomethyl pyrene 120 or 9-

azidomethyl anthracene 121 as ligands. Exemplarily, the CuAAC

reaction is shown for the “click” conjugate 122 using 7-deaza-2’-

deoxy-7-octa-1,7-diynyladenosine (100f) as precursor (Scheme 35).

Functionalization with 3-azido-7-hydroxycoumarin (118) was per-

formed in the presence of CuSO4·5 H2O using sodium ascorbate as

a reducing agent in THF/H2O/t-BuOH (3 : 1 : 1) at room tempera-

ture [180]. Likewise the “click” reaction was performed on the 7-

deazapurine 2’-deoxyribonucleosides 99a, 100a,f and 102f to afford

various fluorescent “click” conjugates (123-129) (Fig. 19) [140,

145, 146, 149, 178, 180-182].

7-Deazapurine “click” conjugates were also subjected to fluo-

rescence studies [139, 140, 145, 146, 181, 182]. It was found that 7-

deazapurine nucleoside dye conjugates show significantly lower

fluorescence than those of corresponding 8-aza-7-deazapurine or

pyrimidine nucleosides; a phenomenon which was studied with 7-

hydroxycoumarin or anthracene as reporter group [181, 182]. Two

examples illustrating these findings are shown in Fig. (20).

The fluorescence properties of compound 128 were investigated

at pH 8.5 as the 7-hydroxycoumarin dye exists predominantly in the

anionic form only under alkaline conditions [182]. The “click” con-

jugate 128 has an excitation maximum at 393 nm with an emission

at 477 nm (Fig. 20a). For comparison, the fluorescence spectrum of

the corresponding 8-aza-7-deaza-2’-deoxyguanosine coumarin

“click” conjugate 130 was measured. Fig. (20b) shows a direct

comparison of the emission spectra of 128 and 130, indicating that

the fluorescence maximum of 128 is about 10-times lower than that

of 130 [182]. Accordingly, the fluorescence properties of the 7-

deaza-2’-deoxyadenosine anthracene “click” conjugate 126 were

compared with those of the corresponding 8-aza-7-deaza-2’-

deoxyadenosine anthracene conjugate 131 [181]. In this case, the

fluorescence intensity of 126 is reduced by around 95% to the 8-

aza-7-deaza-2’-deoxyadenosine conjugate 131 (Fig. 20c). Quench-

ing within the 7-deazapurine conjugates 126 and 128 was attributed

to a charge transfer between the respective nucleobase and the dye.

Due to their low oxidation potential, 7-deazapurine nucleosides

quench the fluorescence of a dye significantly, while this is not the

case for the corresponding 8-aza-7-deazapurine conjugates (130,

131); most likely due to their higher oxidation potential [139, 181,

182].

In a very recent report, 7-deaza-2’-deoxy-7-ethynyladenosine

100a was conjugated to the spin label 4-azido-2,2,6,6-tetramethyl-

piperidine-1-oxyl (132; 4-azido TEMPO) [183] by applying the

CuAAC reaction [184]. Compound 100a was functionalized with

132 by the “click” reaction in the presence of CuI in a 3:1:1 mixture

of THF/t-BuOH/H2O (Scheme 36). In this case, CuI has been used

as copper(I) source instead of the Cu(II)SO4/ascorbic acid system

(see Scheme 35 for comparison) to avoid reduction of the nitroxide

radical by ascorbic acid to the non-paramagnetic hydroxylamine

derivative during “click” reaction [184]. Addition of N,N-

diisopropylethylamine (DIPEA) was essential for the completion of

the reaction within 4 h. The spin labeled 1,2,3-triazolyl nucleoside

conjugate 133 was obtained in 64%.

O

N3

OH

N3

O

121118

N3

120

O

N3

OMeO

119

N3

117

Fig (18). Reporter groups employed in the “click” reaction with 7-deazapurine 2’-deoxyribonucleosides.

O

HO

N

N N

HO

NH2

N

N

N

OO

OH

122

CuSO4 5 H2O

Na-ascorbate

THF:H2O:t-BuOH,

3:1:1+ 118

O

HO

N

N N

HO

NH2

100f

33%

Scheme 35.


123 (25%)

O

HO

N

N N

HO

NH2

N

N

N

O

HO

HN

N N

HO

O

N

N

N

OO

OH

126 (78%) 127 (85%)

O

HO

HN

N N

HO

O

N

N

N

O

HO

HN

N N

HO

O

N

N

N

OO

OH

129 (83%)128 (53%)

H2N H2N

O

HO

N

N N

HO

NH2

N

N

N

OO

OMe

124 (48%)

O

HO

HN

N N

HO

O

N

N

N

125 (66%)

H2N

O

HO

N

N N

HO

NH2

N

N

N

OO

OH

Fig (19). Fluorescent “click” conjugates.

(a) (b)

O

HO

N

N N

X

HO

NH2

N

N

N

126: X = CH

131: X = N

O

HO

HN

N N

X

HO

O

N

N

N

OO

OH

128: X = CH

130: X = N

H2N

(c) (d)

Fig (20). (a) Excitation and emission spectra of the 7-deaza-2’-deoxyguanosine coumarin “click” conjugate 128 and (b) direct comparison of the emission

spectra of the coumarin “click” conjugates 128 and 130. Measured in a mixture of DMSO (0.5 ml) and 99.5 ml of 0.1 M Tris-HCl buffer at pH 8.5 with a con-

centration of 9.4 10-3

mol/l [182]. (c) Direct comparison of the emission spectra of anthracene “click” conjugates 126 and 131. Measurements were performed

at identical molar concentration (0.98 M) in methanol [181].


O

HO

N

N N

HO

NH2

133

+

O

HO

N

N N

HO

NH2

100a

N

N

N

NO

CuI, DIPEA, rt,

THF:H2O:t-BuOH, 3:1:1

N

O

N3

132

64%

Scheme 36.

Fig (21). (a) and (c) molecular dynamics (MD) simulation snapshots of a DNA duplex containing two spin labeled residues of 133 within one of the strands. (c)

Spin spin distance for the respective duplex determined for the oxygen atoms of the nitroxides [184].

Functionalization of 100a was performed on nucleoside level

and on 100a being a constituent of DNA oligonucleotides, allowing

accessibility to study continuous wave (cw) and pulse EPR spec-

troscopy. Interspin distances were studied on single-stranded oli-

gonucleotides and duplexes incorporating two spin labeled “click”

conjugates (133) at distant positions (Fig. 21) or when 133 was a

component of a modified ‘dA-dT’ base pair within an oligonucleo-

tide duplex [184]. By applying cw and pulse EPR spectroscopy,

interspin distances in the 1-2 nm range were obtained with high

accuracy. It was suggested that the spin labeled DNA system ob-

tained via “click” reaction has the potential to provide detailed in-

sights into structural changes caused by unusual DNA structures, by

mispairing, DNA damages and/or lesions [184].

Due to the ongoing interest of high density labelling of nucleo-

sides and oligonucleotides, tripropargylamine – a branched side

chain with two terminal triple bonds – was introduced at position-7

of 7-deaza-2’-deoxyadenosine and 7-deaza-2’-deoxyguanosine (

99k, 100k; see Scheme 32, section 4.1). As both bonds can be func-

tionalized simultaneously (“double click” reaction), the density of

labelling is increased. The “double click” reaction was performed in

THF/t-BuOH/H2O (3 : 1 : 1) in the presence of CuSO4·5 H2O and

sodium ascorbate as described for the “mono”-alkynylated com-


pounds, employing benzylazide 117, 3-azido-7-hydroxycoumarin

118, 1-azidomethyl pyrene 120 or 9-azidomethyl anthracene 121 as

ligands [140, 179]. Scheme 37 shows the “double click” reaction

using the 7-tripropargylamine derivative of 7-deaza-2’-

deoxyguanosine 99k as precursor to afford the nucleoside pyrene

conjugate 134 (79% yield) [140].

To evaluate the photophysical properties, the excitation and

emission spectra of the “double click” product 134 (tripropargy-

lamine pyrene conjugate) were measured and compared to those of

129 (octadiynyl pyrene conjugate; Fig. 19) and the abasic octyne

derivative 135. The abasic derivative 135 contains all necessary

elements of the dye conjugate except 7-deazaguanine (Fig. 22)

[140]. Fig. (22) indicates that only the “double click” product 134

with two proximal pyrenes shows strong excimer fluorescence (464

nm) and rather low monomer fluorescence at 377 nm and 394 nm,

while the conjugate 129 containing one pyrene shows only mono-

meric pyrene emission. Monomeric pyrene emission was also ob-

served for the abasic octyne derivative 135. From this, it was con-

cluded that in “double click” conjugate 134 the two pyrenes are in

proximal position thereby developing strong excimer fluorescence.

From Fig. (22) it is also apparent that both nucleoside pyrene con-

jugates (129 and 134) show rather low monomer fluorescence com-

pared to the abasic conjugate 135. These findings point to a quench-

ing of the pyrene fluorescence by the 7-deazaguanine moiety within

O

HO

HN

N N

HO

O

H2N

N

CuSO4, sodium ascorbate

THF:H2O:t-BuOH, 3:1:1, rt

79%

99k

+

O

HO

HN

N N

HO

O

H2N

N

N

N

N

NN

N

134

120

Scheme 37.

Fig (22). The excitation and emission spectra of “click” conjugates 129, 134 and 135 in methanol. All conjugates were excited at 340 nm, and the concentra-

tion of the “click” conjugates was identical (6.8 x 10-6

M.) [140].


both nucleoside conjugates which was attributed to an intramolecu-

lar charge transfer [140].

4.1.2. Cross-linking of 7-Deazapurine 2’-Deoxyribonucleosides

The “click” reaction has also been applied to crosslink DNA

strands; a “hot” topic of current research [185-189]. For that, azido

groups as well as terminal triple bonds were introduced at the ter-

mini of oligonucleotides and the “click” reaction was induced with

copper(I) salts by post-modification. Very recently, a novel proto-

col for the cross-linking of DNA strands was developed by our

laboratory [190]. Oligonucleotides incorporating constituents with

alkynylated side chains at a terminal or internal position were se-

lected for cross-linking by a “bis-click” reaction. Through this tem-

plate-free procedure, two identical strands can be linked together by

using bis-azides such as 136 or 138. A stepwise procedure was also

developed, where in the first step only one azido group was reacted

to give a triazole mono-functionalized oligonucleotide conjugate

bearing still another reactive azido group. Consequently, this inter-

mediate has the potential to be cross-linked in a second step with

another strand of any type of DNA bearing an alkynyl group. This

protocol was used to synthesize both identical as well as non-

identical cross-linked oligonucleotides [190], and can also be ap-

plied to nucleosides [149, 178, 190].

The “bis-click” reaction was performed on the 7-octadiynylated

nucleosides 99f and 100f with the respective bis-azides 136 and 138

to give the cross-linked products 137 and 139, respectively

(Scheme 38) [149, 178]. The cross-linking reaction of 99f was car-

ried out in the presence of CuSO4·5 H2O/sodium ascorbate in

THF/t-BuOH/H2O (3:1:1) and afforded 137 in 40% yield, while

CuI, DIPEA in THF/t-BuOH/H2O were used for the cross-linking

of 100f to give 139 in 54% yield.

4.1.3. Functionalization of 7-Deazapurine 2’-Deoxyribonucleo-

sides by Other Methods

Several 7-deazapurine ribonucleosides, such as queuosine

(140), epoxy-queuosine (141) or galactosyl-queuosine (142) (Fig.

HN

N N

O

H2N

+

136

HN

N N

O

H2N

N

N

N

HN

NN

O

H2N

N

N

N

CuSO4 5 H2O

sodium ascorbate,

.

THF/t-BuOH/H2O,

O

HO

HO

O

HO

HO

O

HO

HO

N3 N3

99f 137

N

N N

NH2 CuI, DIPEA, rt, 12h

N

N N

NH2

N

N

N

+

THF/t-BuOH/H2O,

3:1:1

54%

139

N

NN

NH2

N

N

N

O

HO

HO

O

HO

HO

O

HO

HO

100f

S

O

O

S

O

O

N3N3

138

3:1:1, rt, 16h, 40%

Scheme 38.


23), are found in transfer RNAs (tRNAs) [191], and carry 7-

substituents which represent Mannich bases. Corresponding 2’-

deoxyribonucleosides are not naturally occurring. Therefore, it was

of interest to transfer this structural motif into DNA constituents.

Moreover, the Mannich base can be used to introduce reporter

groups into position-7 of 7-deazapurine 2’-deoxyribonucleosides.

In principle, 7-deazapurine nucleosides with Mannich bases as

side chains are accessible by two routes, (i) glycosylation of a suit-

able nucleobase precursor already carrying the Mannich side chain

or (ii) by the Mannich reaction performed on a 7-deazapurine nu-

cleoside. As the solubility of Mannich bases is low in MeCN (nu-

cleobase anion glycosylation), route (ii) was followed [192].

The Mannich reaction was performed on 7-deaza-2’-

deoxyadenosine (14a) in an aq. solution of formaldehyde, mor-

pholine and acetic acid at 60°C (conditions I) to afford compound

143 in 43% yield (Scheme 39). In a similar way, the toluoyl pro-

tected 6-methylthio nucleoside 144 was converted into the Mannich

nucleoside 145 (70% yield) [192].

When the same reaction conditions (aq. formaldehyde, mor-

pholine, AcOH as solvent, 60°C; conditions I) were applied to 7-

deaza-2’-deoxyguanosine (12a), decomposition of 12a was ob-

served. When the amount of acetic acid was reduced and the tem-

perature was strictly controlled (60°C; conditions II), the Mannich

nucleoside 146 carrying the side chain at position-8 was isolated

(Scheme 40) [192]. Next, the isobutyrylated compound 147 [193]

O

HO OH

HN

N N

HO

O

H2N

HN

HO

OH

queuosine

140

O

HO OH

HN

N N

HO

O

H2N

HN

HO

OH

141

O

O

HO OH

HN

N N

HO

O

H2N

HN

142

O

OH

O

OH

HO

OH

epoxy-queuosine galactosyl-queuosine

Fig (23).

N

N

R1

O

R2O

N

R2O

14a: R1 = NH2, R2 = H

144: R1 = SMe, R2 = Tol

N

N

R1

O

R2O

N

R2O

N O

aq. HCHO, morpholine,

AcOH, 60°C

143: R1 = NH2, R2 = H

145: R1 = SMe, R2 = Tol

143: 43%

145: 70%

Scheme 39.

HN

N

O

O

R2O

N

R2O

12a: R1 = R2 = H

147: R1 = R2 = iBu

HN

N

O

O

R2O

N

R2O

R3


AcOH, 60°C

146: R1 = R2 = R3 = H, R4 =

148: R1 = R2 = iBu, R3 = H, R4 =

149: R1 = R2 = iBu, R4 = H, R3 =

146: 84%

148: 72%

149: 9%

R1HN R1HN

CH2 N O

R4

CH2 N O

CH2 N O

Scheme 40.


was employed as precursor. The reaction conditions mentioned

above using AcOH as solvent (conditions I) furnished a mixture of

the 8-substituted product 148 (72%) together with a minor amount

of the 7-modified derivative 149 (9%) (Scheme 40).

The Mannich reaction was also performed on the 2-amino-6-

methoxy nucleoside 11a under conditions II (weakly acidic) as

acetic acid when utilized as solvent (conditions I) led to decomposi-

tion of 11a as it was already observed for 12a. The reaction af-

forded only the bis-product 150 while the mono-substituted com-

pound could not be detected (Scheme 41) [192]. In order to reduce

the reactivity of compound 11a, the amino group was protected

with a tosyl residue ( 151), and the reaction was carried out as

described for 11a (conditions II). In this case, the 8-funtionalized

Mannich base 152 was isolated. From these observations it was

concluded that 7-deaza-2’-deoxyguanosine derivatives cannot be

used for the introduction of a Mannich side chain at position-7

[192].

Alternatively, the protected 6-methoxy-2-methylthio-7-

deazapurine 2’-deoxyribonucleoside 153 was used as starting mate-

rial for the Mannich reaction (Scheme 42). Compound 153 was

prepared via nucleobase anion glycosylation (TDA-1, KOH,

MeCN) employing halogenose 7 [192]. Next, the Mannich reaction

(conditions I) was carried out, and nucleoside 154 with the Mannich

side chain attached to position-7 was obtained in high yield (95% of

crude product). Conversion of the OMe group into an oxo group

was performed with trimethylsilyl chloride (TMS-Cl)/NaI in MeCN

to give 155. The free nucleoside 156 was obtained in three steps

which includes treatment of 156 with 3-chloroperbenzoic acid (m-

CPBA) in CH2Cl2 followed by NH3 in dioxane. Finally, deprotec-

tion of the sugar moiety yielded the Mannich nucleoside 156 in

69% [192].

N

N

OMe

O

HO

N

HO

11a: R = H

151: R = Tos

N

N

OMe

O

HO

N

HO

R2


AcOH, 60°C

150: R1 = H, R2 = R3 =

152: R1 = Tos, R2 = H, R3 =

150: 39%

152: 43%

RHN R1HN

CH2 N O

R3

CH2 N O

Scheme 41.

N

N

OMe

O

TolO

N

TolO


AcOH, 60°C

95%

H3CS

N

N

OMe

O

TolO

NH

TolO

H3CS

N

N

OMe

O

TolO

N

TolO

H3CS

Cl

22

7

+

TDA-1, KOH,

MeCN

153

69%

N O

154

HN

N

O

O

TolO

N

TolO

H3CS

N O

155

HN

N

O

O

HO

N

HO

H2N

N O

156

TMS-Cl, NaI,

MeCN

154

1) m-CPBA, CH2Cl2

2) sat. dioxane/NH3

3) NH3, MeOH

90% 69%

Scheme 42.


4.2. 7-Deazapurine 2'-Deoxy-2'-fluoroarabinonucleosides and

2',3'-Dideoxy-3'-fluororibonucleosides

It has been shown that the sugar modification of nucleosides by

a fluorine atom can enhance biological activity as well as the stabil-

ity of the glycosylic bond [194-197]. Fluorinated 7-deazapurine

nucleosides, such as 2’-deoxy-2’-fluoroarabinosangivamycin (157c)

and 2-amino-2’-deoxy-2’-fluoroarabinotubercidin (158a), can act as

antiviral agents [198-200]. Selected 7-deazapurine fluoroarabino-

nucleosides (157-161) are shown in Fig. (24). These nucleosides

have been synthesized by a convergent route using the nucleobase

anion glycosylation. This reaction utilizes a 7-deazapurine base

which is glycosylated with 3,5-di-O-benzoyl-2-deoxy-2-fluoro- -

D-arabinofuranosyl bromide (162) [201]. The nucleobase anion is

generated with sodium hydride (sodium salt glycosylation) or

KOH/TDA-1/MeCN (solid-liquid glycosylation). As the configura-

tion of sugar bromide 162 was established to be -D, and the glyco-

sylation reaction proceeds under stereoselective control, the -D-

nucleosides are the only reaction products.

A reaction sequence is outlined in Scheme 43. The nucleobase

27a was glycosylated with the sugar bromide 162 in dry MeCN in

the presence of NaH furnishing -D-nucleoside 163 exclusively

[199]. Debenzoylation of 163 with NH3/MeOH afforded compound

164a, which on treatment with 0.5 M NaOMe/MeOH gave the 6-

methoxy nucleoside 164b. Demethylation of 164b with io-

dotrimethylsilane in MeCN furnished the guanosine analog 159a.

The thioguanosine derivative 159b was obtained via thiation of 163

with thiourea followed by debenzoylation. In a similar way, the

selenoguanine nucleoside 159c was prepared. Treatment of 163

with selenourea in absolute ethanol ( 165c), followed by deben-

zoylation with NH3/MeOH yielded the selenonucleoside 159c.

Solid-liquid conditions were also applied for the glycosylation

of 7-deazapurines with the fluoro sugar 162 (Scheme 44). The con-

densation of 2-amino-6-chloro-7-deazapurine (27a) with 162 was

performed in MeCN in the presence of TDA-1 and KOH to give the

-D-anomer 163 exclusively. The latter was deblocked yielding the

intermediate 164a. The chloro substituent of compound 164a was

HN

N

X

H2N

OHO

HO

F

N

157a: R = H

b: R = CN

c: R = CONH2

d: R = CSNH2

e: R = F

160a: R = H

b: R = F

158a: R = H

b: R = Cl

c: R = Br

d: R = I

161159a: X = O

b: X = S

c: X = Se

N

N

NH2

OHO

HO

F

N

R

N

N

NH2

OHO

HO

F

N

R

H2N

HN

N

O

OHO

HO

F

N

R

HN

N

NH2

OHO

HO

F

NO

Fig (24).

N

N NH

Cl

H2NN

N

Cl

H2N27a

162 163

OBzO

BzO

F

Br

+

OBzO

BzO

F

N

N

N

R

H2N

OHO

HO

F

N

HN

N

X

H2N

OBzO

BzO

F

N

165b: X = S

c: X = Se

58%

b: thiourea, EtOH

c: selenourea, EtOH

HN

N

X

H2N

OHO

HO

F

N

159b: X = S

c: X = Se

NH3/MeOH

b: 92%

c: 91%

b: 93%

c: 75%

a: NH3/MeOH

b: NaOMe/MeOH

a: 93%

b: 73%

163

Me3SiI,

MeCN

92%

HN

N

O

H2N

OHO

HO

F

N

164a: R = Cl

b: R = OMe

159a

NaH,

MeCN

Scheme 43.


displaced by an amino group ( 158a). Selective deamination at

the 2-amino group yielded 2'-deoxy-2'-fluoro- -D-arabino-

furanosyl-7-deazaisoguanosine (161) [202].

Similarly, glycosylation of 162 with the 7-halogenated 7-deaza-

2-pivaloylaminopurines 41b-d [70] (MeCN/KOH/TDA-1) afforded

-D-nucleosides (Scheme 45). However, this reaction resulted in a

mixture of the N7-linked nucleosides 166b-d and N

2, N

7-

bisglycosylated products 167b-d [202]. This was not observed

when 41b-d were glycosylated with 2-deoxy-3,5-di-O-(p-toluoyl)-

-D-erythro-pentofuranosyl chloride (7) (see section 3.2.3). It was

noticed that the formation of 166b-d required an extended reaction

time due to the decreased reactivity of the fluoro sugar 162. Thus,

product formation occurred under thermodynamic control leading

to two regioisomeric series of reaction products (166b-d and 167b-

d). Compounds 166b-d were converted to the 2,4-diamino deriva-

tives 158b-d (25% aq. NH3/dioxane), and compounds 167b-d were

deblocked with NaOMe/MeOH to yield the 6-methoxy nucleosides

168b-d [202].

The solid-liquid glycosylation of 6-chloro-7-deaza-7-

fluoropurine (33e) with the halogenose 162 (TDA-1/KOH/MeCN)

resulted in the formation of the -D-nucleoside 169e. The latter was

deprotected in 25% aq. ammonia with the concomitant displace-

ment of 6-chloro substituent by an amino group affording the

fluorinated tubercidin derivative 157e (Scheme 46). Compound

169e was also transformed to the 6-methoxy compound 170 using

NaOMe/MeOH. Demethylation of 170 gave the inosine analog

160b (2 N NaOH) [67-69].

In a few cases, the formation of -D-nucleosides was accompa-

nied by small amounts of -anomers. This was the result of an in-

creased reaction temperature [203] or a low nucleophilicity of the

nucleobase allowing the sugar bromide to equilibrate [198]. As the

glycosylation reaction of 33a with the sugar bromide 162 required

20 h for completion, anomerization of the halogenose took place

with the formation of a mixture of the -nucleoside 169a and its -

anomer 171 (Scheme 47), which were separated by silica gel chro-

matography [198]. Debenzoylation of 169a with methanolic am-

monia (room temperature) afforded 172, which upon amination

(NH3/MeOH at 120°C) gave the tubercidin derivative 157a. Thia-

tion of 169a with thiourea in the presence of a catalytic amount of

formic acid followed by debenzoylation afforded 7-deaza-2’-deoxy-

2’-fluoroarabino-6-thioinosine (173). Oxidation of 173 (30%

H2O2/NH3·H2O) gave 7-deaza-2’-deoxy-2’-fluoroarabinoinosine

(160a).

N

N NH

Cl

H2N

27a

162

164a

161

(i) MeCN, TDA-1, KOH

(ii) NH3/MeOH, rt, 18h

aq. NH3,

dioxane

NaNO2,

AcOH/H2O

(i) 59%

(ii) 86%

90% 69%+

158a

N

N

NH2

H2N

OHO

HO

F

N

HN

N

NH2

O

OHO

HO

F

N

Scheme 44.

N

N NH

Cl

PivHN

R

N

N N

Cl

PivHN

N

N N

Cl

N

R

R

41b-d

b: R = Cl; c: R = Br; d: R = I

MeCN, TDA-1, KOH

NaOMe,

MeOH

aq. NH3/dioxane

90°C, 24h

+

OBzO

BzO

F

OBzO

BzO

F

OBzO

BzO

F

Piv

166b-d

167b-d

158b-d

168b-d

b: 87%

c: 90%

d: 86%

b: 89%

c: 90%

d: 82%

166b: 45%; 167b: 11%

166c: 45%; 167c: 10%

166d: 44%; 167d: 12%

N

N N

NH2

H2N

R

OHO

HO

F

N

N N

OMe

H2N

R

OHO

HO

F

162

OBzO

BzO

F

Br

Scheme 45.


Similarly, glycosylation of the sodium salt of 174 [106, 110]

with 162 required a longer reaction time (18 h, rt) or high tempera-

ture (80°C, 4 h) which resulted in the formation of an anomeric

mixture with the -D-anomer 175 as the main product and its -

anomer 176 as minor product (Scheme 48) [198, 203]. Treatment of

175 with NH3/MeOH at room temperature led to ring closure with

concomitant removal of the benzoyl groups affording 8-bromo-7-

cyano-7-deazapurine nucleoside 177. Selective acetylation of 177

with acetic anhydride in the presence of 4-(dimethylamino)pyridine

(DMAP) in DMF gave 3’,5’-di-O-acetyl derivative 178a, which on

reductive debromination (5% Pd/C, MgO, H2), yielded the nucleo-

side 178b. Deacetylation of 178b (Na2CO3 in aq. 1,4-dioxane) fur-

nished the fluorinated 2’-deoxytoyocamycin 157b. Oxidative hy-

drolysis of the 7-carbonitrile group of 157b (30% H2O2/aq. NH3)

yielded 2’-deoxy-2’-fluoroarabinosangivamycin (157c). The corre-

sponding thiosangivamycin 157d was obtained from 157b using

H2S in dry pyridine.

The replacement of a hydroxy group by a fluorine atom in 7-

deazapurine 2’-deoxyribonucleosides can change the N/S-

conformational equilibrium of the pentofuranose moiety. This equi-

librium is driven by various stereoelectronic gauche and anomeric

effects. The sugar pucker is described relative to the exocyclic atom

C5’, and defined as endo if the puckered atom is at the same side of

N

N NH

Cl N

N

Cl

33e

162

TDA-1, KOH,

MeCN, rt, 10 min

+

OBzO

BzO

F

N

169e

F

F

67%

N

N

NH2

OHO

HO

F

N

157e

F

N

N

OMe

OHO

HO

F

N

170

F

HN

N

O

OHO

HO

F

N

160b

F

aq. NH3

72%

NaOMe,

MeOH

97%

2N NaOH

37%

169e

Scheme 46.

N

N NH

ClN

N

Cl

33a 162

NaH, MeCN,

rt, 20hO

BzO

BzO

F

Br+

OBzO

BzO

F

N

OBzO

BzO

F

N

N

Cl

N

HN

N

S

OHO

HO

F

N

+

169a (57%) 171 (9%)

172: R = Cl (72%)

157a: R = NH2 (80%)

(i) thiourea, EtOH

(ii) NaOMe/MeOH NH3/MeOH

84%

169a

N

N

R

OHO

HO

F

N

HN

N

O

OHO

HO

F

N

aq. NH3,

30% H2O2

74%

173160a

Scheme 47.


the plane as C5’, otherwise it is exo. The north (N) conformation is

centered around the C3’-endo conformer, while the south (S) con-

formation is centered around the C2’-endo species (Fig. 25). The

conformational analysis of a series of fluorinated 7-deazapurine

nucleosides has been studied using the PSEUROT program (Table

1) [67, 202, 204].

As shown in Table 1, the presence of the fluorine atom of the

sugar moiety drives the N S equilibrium of 7-deazapurin-2,6-

diamine 2’-deoxy-2’-fluoroarabinonucleosides 158a-d towards N

(34-37% N) in comparison to the corresponding 2’-

deoxyribonucleosides 18a-d (26-28% N) [70, 202]. The same ob-

servation is made for 7-deaza-2’-deoxy-2’-fluoroisoguanosine (161)

(35% N) or 2’-deoxy-2’-fluoroadenosine (FdA) (36% N) and their

corresponding 2’-deoxyribonucleosides 36a (27% N) or dA (28%

N) [70, 202, 204]. This means that a fluorine atom in the 2’-‘up’

position increases the population of the N conformers by around

10%. Only with nucleoside 157e, the change is less pronounced

(3%) [67]. From the view point of the gauche disposition of the 2’-

N

NC

174 162

NaH, MeCN, rt, 18h

or 80°C, 4h

OBzO

BzO

F

Br+

OBzO

BzO

F

N

N

N

NH2

OHO

HO

F

N

OBzO

BzO

F

N

N

N

NH2

OAcO

AcO

F

N

+

175 (50%) 176 (16%)

178a: X = Br (77%)

b: X = H (84%)

177

EtO

CN

Br

CN

Br

CN

X

N

NC

N

EtO

CN

Br

N

N

NH2

OHO

HO

F

N

CN

157c: R = CONH2 (69%)

d: R = CSNH2 (93%)

88%

NH3,

MeOH

Ac2O,

DMAP,

DMF

Na2CO3,

aq. dioxane

96%

Br

CNNC

NEtO

175

Pd/C, H2

157c: aq. NH3,

30% H2O2

157d: H2S, Et3N,

pyridine

N

N

NH2

OHO

HO

F

N

R

157b

Scheme 48.

O

B

5'

C2'-exo-C3'-endo

O

B

C2'-endo-C3'-exo

F

OH

F

HO

4'

3'

2'

1'4'

2'

1'3'

5'

B = Base

HO

HO

N S

Fig (25). N and S conformations of sugar rings of 7-deazapurine 2’-deoxy-2’- fluoroarabinonucleosides.

Table 1. Population of Sugar Conformers of 7-Deazapurine Fluoroarabinonucleosides and 7-Deazpurine 2’-Deoxyribonucleosides

Fluoro-compd Conformation Deoxy-compd Conformation

FdA 36% N dA 28% N [204]

158a 34% N 18a 26% N

158b 36% N 18b 28% N

158c 37% N 18c 29% N

158d 36% N 18d 28% N

161 35% N 36a 27% N

160b 40% N 15e 30% N

157e 33% N 14e 30% N

N

N

NH2

H2N

R

OHO

HO

N

HN

N

NH2

OHO

HO

NO

18a-d 36a

N

N

NH2 F

OHO

HO

N

14e

HN

N

OHO

HO

N

15e

O

N

N

NH2 F

N

N

NH2

H2N

R

OHO

HO

N

OHO

HO

F

N

HN

N

NH2

OHO

HO

F

NO

F

161158a-d 157e

HN

N

OF

OHO

HO

N

F

160b


F

N

N

N

NH2

OHO

HO

N

dA

N

N

N

NH2

OHO

HO

F

N

FdA


‘up’ fluoro substituent with the furanose oxygen, the 2’-‘up’ fluoro

favors the S conformation. However, this puts the F and the 3’-OH

in the ap orientation. Because the 2’-‘up’ fluoro and 3’-OH also

seek to have a gauche orientation, which can be best achieved in the

north conformation, there is a small pull towards N as a conse-

quence of this force.

The fluorinated nucleosides 7-deaza-2’-deoxy-7-fluoro-

adenosine (14e), 7-bromo-2'-deoxy-2,6-diamino-2'-fluoro- -D-

arabinofuranosyl-7-deazapurine (158c) and 7-deaza-7-fluoro-2'-C-

methylinosine (179) were subjected to single-crystal X-ray analysis

by our laboratory [205-207]. As it can been seen from Fig. (26),

nucleoside 179 is a close derivative of the highly active anti-HCV

compound 180 [208].

In the crystal structure of compound 179 (Fig. 27A), the glyco-

sylic bond torsion angle is in the anti range [ = 140.78 (14)°],

while that of 14e (Fig. 27B) is situated between anti and high-anti

[ = 101.1 (3)°]. The 2’-C-methylribofuranosyl moiety of 179

adopts an N sugar conformation with an unsymmetrical twist (C3'-

endo-C2'-exo, 3T2) and P = 5.9 (2)° and m = 42.1 (1)°. On the other

hand, the 2’-deoxyribonucleoside 14e exhibits an S-type sugar con-

formation (2T3) with P = 164.7 (3)° and m = 40.1 (2)°, which is

consistent with the predominat S conformation (70%) observed in

solution (Table 1). In the crystal structure of 158c, two conforma-

tions of the exocyclic C4’-C5’ bond were found, corresponding to

conformer 1 (0.69 occupancy) (Fig. 27C) and conformer 2 (0.31

occupancy) (Fig. 27D). However, both conformers show the same

N

N

NH2

OHO

HO

N

F

N

N

NH2

OHO

HO

F

N

Br

H2N

HN

N

O

OHO

HO

Me

N

F

OH

N

N

NH2

OHO

HO

Me

N

F

OH

179 18014e 158c

Fig (26).

(A) (B)

(C) (D)

Fig (27). Perspective views of (A) 7-deaza-7-fluoro-2'-C-methylinosine (179) [207], (B) 7-deaza-2’-deoxy-7-fluoroadenosine (14e) [205], (C) conformer 1 of

7-bromo-2'-deoxy-2,6-diamino-2'-fluoro- -D-arabinofuranosyl-7-deazapurine (158c) and (D) conformer 2 of 158c [206]. Displacement ellipsoids are drawn at

the 50% probability level and H atoms are shown as spheres of arbitrary size.


anti glycosylic bond torsion angle [ = 114.8 (4)°] and N-type sugar

conformation (3T4) with P = 23.3 (4)° and m = 36.5 (2)°. In this

case, the N-type sugar conformation found for the crystalline state

of 158c is not consistent with the predominant sugar pucker of 158c

observed in solution (63% S, Table 1).

2’,3’-Dideoxy-3’-fluorothymidine (FLT) shows antiviral activ-

ity against HIV; it is even a more potent inhibitor of HIV replica-

tion than AZT. Unfortunately, FLT and related nucleosides were

found to be highly cytotoxic. This prompted us to synthesize 7-

deazapurine 2’,3’-dideoxy-3’-fluoronucleosides such as 181a [209]

and 182a [210] (Scheme 49). The syntheses started from the 2’-

deoxyribonucleosides 183 or 29a. The 5’-hydroxyl groups were

protected with a (tert-butyl)diphenylsilyl residue affording 184a or

184b [211], which were then oxidized with CrO3 yielding 3’-oxo

nucleosides 185a or 185b. The reduction of 185a or 185b with

NaBH4 in EtOH resulted in the formation of compounds 186a or

186b having the 3'-hydroxyl group in the arabino configuration.

After protection of the 2-amino group of 186b with a mono-

methoxytrityl (MMT) residue ( 186c), the fluorine substituent

was introduced using (diethylamino)sulfur trifluoride (DAST) with

inversion of configuration ( 187a or 187b). Desilylation of com-

pound 187a with TBAF ( 188a) followed by amination with aq.

NH3 afforded 2’,3’-dideoxy-3’-fluorotubercidin 181a. In the other

route, the trityl residue of 187b was removed with 80% AcOH to

give 187c, which was treated with TBAF ( 188b), followed by 2

M NaOH thereby yielding 7-deaza-2’,3’-dideoxy-3’-

fluoroguanosine 182a. The triphosphates 181b or 182b were pre-

pared from 181a or 182a with POCl3 ( monophosphate) followed

by condensation with tetrabutylammonium diphosphate according

to the one-pot protocol of Ludwig (see also Scheme 59, section

4.3.4) [212]. Both triphosphates (181b, 182b) were found to be

inhibitors of HIV-1 reverse transcriptase (see Table 2, section

4.3.4).

O

N

N N

HO

Cl

183: R = H

29a: R = NH2

R

HO

O

N

N N

BuPh2SiO

Cl

184a: R = H

b: R = NH2

R

HO

tO

N

N N

BuPh2SiO

Cl

185a: R = H

b: R = NH2

R

t

O

O

N

N N

BuPh2SiO

Cl

186a: R = H

b: R = NH2

R

tOH

O

N

N N

BuPh2SiO

Cl

187a: R = H

b: R = NHMMT (29%)

R

t

F

tBuPh2SiCl

imidazole, DMF

CrO3, pyridine

Ac2O, CH2Cl2

186c: R = NHMMT (94%)

MMT-Cl, pyridine

NaBH4, EtOH

80% AcOH

187c: R = NH2 (73%)

O

N

N N

HO

Cl

R

F

188a: R = H

b: R = NH2

O

N

N N

RO

NH2

F

DAST,

CH2Cl2 or toluene

TBAF, THF

181a,b 182a,b

or

181a: aq. NH3/dioxane

182a: 2M NaOH

O

HN

N N

RO

F

H2N

O

a: 76%

b: 68%

a: 57%

b: 35%

a: 76%

b: 92%

P O

O

OH

P O P OH

O O

OH OH

181a: 76%

182a: 36%

b: R =a: R = H

Scheme 49.


4.3. 7-Deazapurine 2’,3’-Dideoxyribonucleosides

2’,3’-Dideoxyribonucleoside triphosphates can act as termina-

tors of DNA-polymerase as well as of reverse transcriptase [213-

216]. Therefore, several purine and pyrimidine 2’,3’-

dideoxyribonucleosides show antiviral activity against RNA and

DNA viruses such as human immunodeficiency virus (HIV) [217-

219] and the Hepatitis B virus (HBV). Their triphosphates are also

used in the Sanger dideoxy sequencing of DNA [21, 220] which is a

standard tool of modern molecular biology. This method has been

modified in several ways. The replacement of dGTP by 7-deaza-

dGTP has been shown to resolve band compression during electro-

phoretic separation [19]. 7-Deazapurine 2’,3’-dideoxyribo-

nucleoside triphosphates bearing a fluorescent dye at position-7

serve as terminators in most currently available automated DNA

sequencing machines [221].

4.3.1. 7-Deazapurine 2’,3’-Dideoxyribonucleosides Used in DNA-

Sequencing

In 1987, Prober and coworkers reported on an improved Sanger

protocol which makes use of modified dideoxyribonucleoside

triphosphates bearing fluorescent dyes in the side chains [21]. The

fluorescent chain terminators can carry different labels for the four

different triphosphates used in the fluorescence-based automated

DNA sequencers [21, 222-225]. Succinylfluorescein has been at-

tached via an aminopropargyl linker to the 5-position of pyrimidi-

nes and to the 7-position of 7-deazapurines. The syntheses of the

triphosphates 189 and 190 are outlined in Schemes 50 and 51. The

protected 2’,3’-dideoxyribonucleoside 191 or 198 served as starting

material [22]. Iodination of 191 and 198 was performed with N-

iodosuccinimide (NIS) in DMF or ICl in CH2Cl2 affording 192 or

199. Then, the methoxy group of 192 was cleaved with sodium

(i) 3 POCl3, H2O, (MeO)3PO

(ii) H2P2O72-(Bu3NH+)2, NBu3

(iii) Et3NHHCO3, H2O

O

HN

N N

O

197

O

POPOPHO

O O O

OOO

C CCH2NH2

Pd(0)(PPh3)4, CuI, Et3N, DMF

CCH2NHCOCF3,HC

N

O CH3

O

O OAcO

O

H2N

O

HN

N N

O

O N

N

O CH3

O

O OO

POPOPHO

O O O

OOO

4 Et3NH+

189

O

HN

N N

HO

CO

H2N

CCH2NHCOCF3

O

N

N N

TrO

OMe

O

N

N N

TrO

OMe

O

HN

N N

TrO

O

O

HN

N N

TrO

O

O

HN

N N

HO

O

NIS, DMF

191 192 193

194 195b

MeS MeS

I

Na thiocresolate,

HMPA, toluene

MeS

1) m-CPBA, CH2Cl2

2) NH3, dioxane

96%

I

97%

70%

AcOH

81%

II

H2N H2N

H2N

196

3 Et3NH+

N

O

O

H

Scheme 50.


thiocresolate ( 193), which was followed by oxidative conversion

of the methylthio group into an amino group to yield 194. The pro-

tected 194 as well as 199 were deblocked affording the 7-iodinated

dideoxyribonucleosides 195b or 200b as central intermediates [22].

Sonogashira cross coupling (CuI, CPd(0)(PPh3)4, Et3N, DMF) of

the 7-iodo nucleoside 195b with N-trifluoroacetylpropargylamine

gave 196 [226]. The latter was converted into its 5’-triphosphate

and deacylated to afford 7-(3-amino-1-propynyl)-7-deaza-2’,3’-

dideoxyguanosine 197. The amino side chain was reacted with O-

acetyl protected succinylfluorescein and deprotected to give 189. In

a similar way, 7-deaza-2’,3’-dideoxy-7-iodoadenosine (200b) was

transformed into the corresponding fluorescence-labeled Sanger

sequencing reagent 190 (Scheme 51).

Sequencing by synthesis (SBS) – as the Sanger sequencing – is

based on the polymerase chain reaction [129-133]. In SBS, a primer

is extended on a template by a single nucleotide, and the identity is

determined by the use of fluorescent reporter groups. Four nucleo-

tides are designed with dyes attached to the 5-position of

pyrimidine nucleotides or the 7-position of 7-deazapurine nucleo-

tides. The dyes are linked to the base via photocleavable linkers and

are cleaved by light (355 nm). Various photo-cleavable linkers have

been developed. The part of the linker which stays on the growing

oligonucleotide chain should be as small as possible. A small cap-

ping group is employed for the 3’-OH position. After nucleotide

identification, the 3’-OH protecting groups are removed chemically.

Allyl groups can be used for that purpose and are stepwise removed

under palladium assistance. As purine nucleotide surrogates, 7-

deazapurine nucleotides are used. 7-Deaza-2’-deoxyadenosine and

7-deaza-2’-deoxyguanosine conjugates 202 and 205 bearing fluo-

rescent dyes and their photochemical cleavage is outlined in

Scheme 52.

7-Deazapurine 2’,3’-dideoxyribonucleosides were also used in

recently developed DNA sequencing approaches [227], such as

MALDI-TOF mass spectrometry DNA sequencing [228]. This

approach makes use of biotinylated 7-deazapurine 2’,3’-

dideoxyribonucleosides 206 and 207 to generate Sanger sequencing

termination products (Fig. 28). The biotin-streptavidin interaction is

used to capture the biotinylated DNA fragments on a streptavidin-

coated solid support followed by direct detection with matrix-

O

N

N N

O

201

NH2

POPOPHO

O O O

OOO

C CCH2NH2

N

O CH3

O

O O

CH3

AcO

H3C

O

O

N

N N

NH2 N

N

O CH3

O

O OO

OPOPOPHO

O O O

OOO

4 Et3NH+

190

O

N

N N

PivO

Cl

O

N

N N

PivO

Cl

O

N

N N

HO

NH2

ICl, Na2CO3, CH2Cl2

198 199

200b

I

NH3, MeOH

70%

I

70%

3 Et3NH+

H3C CH3

N

O

O

H

Scheme 51.


O

HN

N N

O NH

OPOPOPO

O O O

OOO

202

HN

O

O2N

O

O

H2N

N

B

N

F F

CH3

CH3

O

O

N

N N

NH2 NH

O

OPOPOPO

O O O

OOO

205

NN

COO

HN

O

O2N

O

O

O

O

HN

N N

O NH2

OPOPOPO

O O O

OOO

203

H2N

O

HN

O

O2N

CH3

N

B

N

F F

CH3

CH3

+ CO2

+

irradiation at 355 nm,

10 sec

O

O

HN

N N

O NH2

OPOPOPO

O O O

OOO

204

H2N

HO

Pd-deallylation,

30 sec

Scheme 52.


O

N

N N

O

NH2

POPOPHO

O O O

OOO

N

NH

O

OH

S

NHHN

HH

O

206

O

HN

N N

O

O

POPOPHO

O O O

OOO

N

NH

O

OH

S

NHHN

HH

O

207

H2N

Fig (28).

O

HO

N

N N

HO

Cl

O

HO

N

N N

DMTO

Cl

O

PhOCO

N

N N

DMTO

Cl

O

N

N N

DMTO

Cl

O

N

N N

HO

Cl

200a: R = NH2 (65%)

213: R = OMe (78%)

DMT-Cl,

pyridine

ClCOPh,

S

MeCN

n-Bu3SnH,

AIBN

80% AcOH

200a: aq. NH3

213: NaOMe/MeOH

208a: 2N NaOH

183 209 210

211 212a

78% 76% 75%

67%

O

HN

N N

HO

O

or

O

N

N N

HO

R

208a (80%)

S

Scheme 53.

assisted laser desorption ionization time-of-flight mass spectrome-

try (MALDI-TOF MS).

4.3.2. Synthesis of 7-Deazapurine 2’,3’-Dideoxyribonucleosides

7-Deazapurine 2’,3’-dideoxyribonucleosides [61, 211, 229-231]

have been prepared from the corresponding 2’- or 3’-

deoxyribonucleosides as described for the formation of 2’-

deoxyribonucleosides from ribonucleosides (see section 3.3), as

well as by elimination of a 3’-mesyloxy group yielding unsaturated

nucleosides [95], which were subjected to catalytic hydrogenation

[119-122].

2’,3’-Dideoxytubercidin (200a) and 7-deaza-2’,3’-

dideoxyinosine (208a) were prepared by Barton-McCombie deoxy-

genation of the corresponding 2’-deoxyribonucleosides (Scheme

53) [61]. The 5’-hydroxyl group of compound 183 was selectively

protected with a DMT residue (DMT-Cl) to give 209. The 3’-

hydroxyl group of compound 209 was derivatized with phe-

noxythiocarbonyl chloride to give 210 (see also section 3.3).

Treatment with tri-n-butylstannane in toluene in the presence of

AIBN afforded 2’,3’-dideoxyribonucleoside 211. Detritylation of

211 gave the nucleoside 212a, which was further converted to


2’,3’-dideoxytubercidin (200a), the 6-methoxy derivative 213, and

7-deaza-2’,3’-dideoxyinosine (208a).

The 7-deazapurine 2’,3’-dideoxyribonucleoside 200a was also

synthesized by deoxygenation of 3’-deoxyribonucleosides (Scheme

54) [230]. 7-Deazacordycepin (214) was employed as starting mate-

rial and was prepared as described earlier [119, 232]. Compound

214 was converted to 215 with monomethoxytrityl chloride (MMT-

Cl) in pyridine using silver nitrate as a catalyst. The phenoxythio-

carbonyl derivative 216 was prepared next. Barton-McCombie de-

oxygenation of 216 with tri-n-butylstannane in benzene in the pres-

ence of AIBN afforded the 2’,3’-dideoxyribonucleoside 217 which

was deprotected to give 2’,3’-dideoxytubercidin (200a).

The protocols discussed above require sufficient amounts of the

corresponding 7-deazapurine ribo-, 2’- or 3’-deoxyribonucleosides.

This problem was circumvented by the nucleobase anion glycosyla-

tion of various 7-deazapurines employing 2,3-dideoxy-5-O-[(1,1-

dimethylethyl)dimethylsilyl]-D-glycero-pentofuranosyl chloride

(218a) or 2,3-dideoxy-5-O-[(1,1-dimethylethyl)diphenylsilyl]-D-

glycero-pentofuranosyl chloride (218b) [233-236] as activated

sugar components. Compounds 218a,b were prepared in situ from

the corresponding lactol [233] by Appel chlorination [237, 238].

The nucleobase anions of compounds 33a or 27a were gener-

ated under solid-liquid phase transfer conditions (KOH/TDA-

1/MeCN) and were reacted with the anomeric mixture of the sugar

halide 218a resulting in the -anomers 219a,b and the correspond-

ing -nucleosides 220a,b [236] (Scheme 55). Deprotection of

219a,b or 220a,b was performed with TBAF in THF to afford the

free nucleosides 212a, 221a or 222a,b in a total yield of 67-85%

[235, 236]. Further conversion of 212a or 221a provided 7-

deazapurine 2’,3’-dideoxyribonucleosides 200a, 208a, 223a, 224a

and 195a [61, 211, 231] (Scheme 55).

4.3.3. Synthesis of 7-Deazapurine 2’,3’-Didehydro-2’,3’-Dide-

oxyribonucleosides

Since 2’,3’-unsaturated nucleosides, such as d4T and d4C show

antiviral activity [239, 240], the synthesis of modified purine 2’,3’-

didehydro-2’,3’-dideoxyribonucleosides and their corresponding

triphosphates became of interest [95, 121, 210]. In this context, the

synthesis of the 2’,3’-didehydro-2’,3’-dideoxy analogs of tubercidin

(227a), toyocamycin (227f) and sangivamycin (227j) was carried

out starting from their parent ribonucleosides 89a,f,j (Scheme 56)

[121]. Treatment of 89a,f,j with 2-acetoxy-2-methylpropionyl bro-

mide led to a mixture of 2’-O-acetyl-3’-bromo-3’-deoxy sugar

modified nucleosides and corresponding 5’-trimethyldioxolanone

derivatives in the case of 89f and 89j. The addition of methanol

resulted in a complete removal of the 5’-trimethyldioxolanone moi-

ety to yield the 5’-hydroxyl derivatives. Subsequent acetylation

gave the 2’,5’-diacetylated compounds 225a,f,j. Treatment of

225a,f,j with a zinc-copper couple in DMF furnished the 5’-

acetylated 2’,3’-unsatured nucleosides 226a,f,j. Compounds

226a,f,j were deprotected (NH3/MeOH) to give the target nucleo-

sides 2’,3’-dideoxy-2’,3’-didehydrotubercidin (227a), 2’,3’-

dideoxy-2’,3’-didehydrotoyocamycin (227f), and 2’,3’-dideoxy-

2’,3’-didehydrosangivamycin (227j).

The 7-deazapurine nucleosides 233a and 234a, related to 2-

amino-7-deazaadenosine and 7-deazaguanosine, were synthesized

as shown in Scheme 57. 2-Amino-6-chloro-7-deazapurine 2’-

deoxyribonucleoside 29a was utilized as starting material. The 5’-

hydroxyl group of 29a was protected with a (t-Bu)Ph2Si residue to

afford compound 184b. Protection of 184b with dimethylforma-

mide diethyl acetal gave the labile amidine 228. Compound 228

was subjected to hydrolysis (MeOH/H2O) affording the formyl

derivative 229 (75% yield). Treatment of 229 with methanesulfonyl

chloride gave 230. Elimination of the mesyl group and deprotection

of 230 occurred simultaneously with TBAF/THF to give the the

2’,3’-didehydro-2’,3’-dideoxyribonucleoside 231 in 60% yield.

Then, the formyl group was removed (aq. NH3, dioxane) to give

232a. Further displacement of the chloro substituent of 232a (2 M

NaOH) afforded 234a, and nucleophilic displacement with 25% aq.

ammonia yielded 233a.

The isoinosine analog 238 was prepared according to Scheme

58 using the 2-methoxy nucleoside 61 as starting material [95]. The

synthetic route was performed as described above yielding the in-

termediate 237. Treatment of 237 with 2 N NaOH furnished 2',3'-

dideoxy-2'-3'-didehydro isoinosine derivative 238 (81% yield).

O

N

N N

HO

NH2

O

N

N N

MMTO

NH2

O

N

N N

MMTO

NH2

O

N

N N

MMTO

NH2

O

N

N N

HO

NH2

MMT-Cl, AgNO3,

THF/pyridine

ClCOPh,

S

MeCN/DMAP

Bu3SnH,

AIBN, benzene 80% AcOH

214 215 216

217 200a

72% 75%

90% 88%

OH OCOPh

S

OH

Scheme 54.


O

N

N N

SiO

Cl

33a: R = H

27a: R = NH2

218a

N

N NH

Cl

+

219a: R = H (46%)

b: R = NH2 (22%)

N

NN

Cl

O

N

N N

HO

Cl

212a: R = H (67%)

221a: R = NH2 (85%)

OHO

N

NN

Cl

O

SiOO

SiOCl

222a: R = H (82%)

b: R = NH2 (79%)

TBAF/THF

TBAF/THF

KOH,TDA-1

MeCN

R

R

R

R

R

220a: R = H (18%)

b: R = NH2 (20%)

O

N

N N

HO

NH2

O

N

N N

HO

NH2

H2N

O

HN

N N

HO

O

H2N

O

HN

N N

HO

O

O

HN

N N

HO

S

200a 224a 195a208a 223a

( / )

Scheme 55.

O

HO

N

N N

HO

NH2

OH

O

N

N N

AcO

NH2

OAc

AcO

Br

O

MeCN

(i)

(ii) MeOH for 89f,j

(iii) Ac2O/pyridine

Br

O

N

N N

AcO

NH2

Zn-Cu,

DMF

89a,f,j 225a,f,j

O

N

N N

HO

NH2

226a,f,j 227a,f,j

NH3/MeOH

a: R = H; f: R = CN; j: R = CONH2

R R R R

Scheme 56.

4.3.4. 7-Deazapurine 2’,3’-Dideoxyribonucleosides as Inhibitors

of DNA Polymerases

2’,3’-Dideoxyribonucleoside triphosphates act as terminators of

various DNA-polymerases and of viral reverse transcriptase [213-

216]. Therefore, several purine and pyrimidine 2’,3’-

dideoxyribonucleoside show antiviral activity by inhibiting the

growth of the human immunodeficiency virus (HIV) or the Hepati-

tis B virus (HBV) [217-219, 241]. Nucleobase as well as sugar

modified purine and pyrimidine 2’,3’-dideoxyribonucleosides have

been synthesized to improve the toxicology profile. Thus, a number

of 7-deazapurine 2’,3’-dideoxyribonucleotides and their 2’,3’-

didehydro or 2’,3’-dideoxy-3’-fluoro triphosphate analogs have


O

N

N N

HO

Cl

H2N

HO

O

N

N N

BuPh2SiO

Cl

H2N

HO

t

tBuPh2SiCl,

imidazole, DMF

O

N

N N

BuPh2SiO

Cl

(H3C)2NCH=N

HO

t

(H3C)2NCH(OC2H5)2,

DMF

MeOH,

H2O

O

N

N N

BuPh2SiO

Cl

HCHN

HO

t

O

O

N

N N

BuPh2SiO

Cl

HCHN

MsO

O

O

N

N N

HO

Cl

R-HN

CH3SO2Cl,

pyridine

t

(i) TBAF, THF

(ii) 25% aq. NH3,

dioxane

O

HN

N N

HO

O

H2N

29a 184b 228

75%

229 230

93%

O

N

N N

HO

NH2

H2N 2M NaOH

55%

25% aq. NH3,

dioxane

40%

231: R = HCO

232a: R = H

234a233a

231: 60%

232a: 55%

232a

Scheme 57.

O

HO

N

N N

HO

MeO

O

HO

N

N N

BuPh2SiO

MeO

O

MsO

N

N N

BuPh2SiO

MeO

O

N

N N

HO

MeO

O

HN

N N

HO

O

BuPh2SiCl,

pyridine MsCl, pyridine

TBAF/THF 2N NaOH

61 235 236

237 238

89% 82%

96% 81%

t

t t

Scheme 58.

been prepared (Fig. 29), and their activity data against HIV-1 re-

verse transcriptase are given in Table 2.

Fig. (29) displays a series of nucleoside triphosphates (181b,

182b, 200b, 208b, 212b, 223b, 224b, 195b, 234b, 233b, 239, or

232b) which were prepared from the corresponding nucleosides

181a, 182a, 200a, 208a, 212a, 223a, 224a, 195a, 234a, 233a, 227a,

or 232a in an one-pot reaction following a protocol originally de-

veloped for the phosphorylation of purine and pyrimidine 2’-

deoxyribonucleosides by Ludwig (Scheme 59) [212, 235]. The

nucleosides were dissolved in PO(MeO)3 (0°C). Two equivalents of

POCl3 were added resulting in the formation of an activated dichlo-

rophosphate which was directly condensed with bis-

tetrabutylammonium pyrophosphate. Purification on a DEAE-

Sephadex column with aq. triethylammonium bicarbonate yielded


the triphosphates in the form of their triethylammonium salts (Fig.

29).

The 7-deazapurine triphosphates shown in Table 2 were found

to be strong inhibitors of HIV-1 reverse transcriptase. 7-

Deazaguanine, 7-deazaadenine, and 2-amino-7-deazaadenine 2’,3’-

dideoxyribonucleoside triphosphates (195b, 200b, and 224b), their

2’,3’-didehydro analogs (234b, 239, and 233b) and 3’-fluorinated

derivatives (181b and 182b) show similar inhibitory activity against

HIV-1 reverse transcriptase as the corresponding purine 2’,3’-

dideoxyribonucleotides. In the case of compounds 212b, 7-deaza-

2’,3’-dideoxyinosine (208b), and its thio analog 223b less activity

was observed.

O

N

N N

HO

(i) POCl3, PO(MeO)3

(ii) H2P2O72-(Bu3NH+)2

200a

NH2

O

N

N N

O

200b

NH2

POPOPHO

O O O

OHOHOH

30-50%

Scheme 59.

O

N

N N

RO

NH2

O

N

N N

RO

NH2

H2N

O

HN

N N

RO

O

H2N

O

HN

N N

RO

O

O

HN

N N

RO

S

200a,b

224a,b 195a,b

208a,b 223a,b

a: R = H; 239, or b: R = P O

O

OH

P O P OH

O O

OH OH

O

N

N N

RO

NH2

227a or 239

O

N

N N

RO

NH2

H2N

233a,b

O

HN

N N

RO

O

H2N

234a,b

O

N

N N

HO

Cl

232a,b

H2N

O

N

N N

RO

Cl

212a,b

O

N

N N

RO

NH2

181a,b

O

HN

N N

RO

O

H2N

182a,b

F F

Fig (29).

Table 2. Inhibition of HIV-1 Reverse Transcriptase (RT) by Pyrrolo[2,3-d]pyrimidine and Purine 2’,3’-Dideoxyribonucleoside Triphosphates a [210,

235]

IC50 [μM] IC50 [μM] IC50 [μM]

212b 102.0 195b 0.12 239 0.53

200b 0.39 181b 0.43 AZTTP b 0.5

208b 20.0 182b 0.27 ddATP b 0.45

223b 1680.0 234b 0.09 ddGTP b 0.2

224b 0.5 233b 0.39

a The RT inhibitory tests were performed in the laboratories of Boehringer Mannheim GmbH.

b AZTTP = 3’-azido-3’-deoxythymidine 5’-triphosphate; ddATP = 2’,3’-dideoxyadenosine 5’-triphosphate; ddGTP = 2’,3’-dideoxyguanosine 5’-triphosphate.


The inhibitory experiments indicate that a number of 7-

deazapurine 2',3'-dideoxyribonucleoside triphosphates display

strong inhibitory activity against HIV-1 reverse transcriptase in

enzymatic inhibitor assays. However, none of them was a powerful

inhibitor of the HIV virus growth in cellular assays. Probably, 7-

deazapurine 2’,3’-dideoxyribonucleosides withstand phosphoryla-

tion by cellular kinases but immediately form the monophosphates

acting as kinase inhibitors as it was reported for 7-deazapurine ri-

bonucleosides [242, 243]. Pronucleotide derivatives of monophos-

phates might overcome this activity barrier.

5. SYNTHESIS OF 7-DEAZAPURINE -L 2'-DEOXYRIBO-

NUCLEOSIDES

L-Nucleosides, the enantiomers of the naturally occurring D-

compounds are not recognized by mammalian enzymes but are

accepted by some bacteria- or virus-encoded enzymes. This results

in minimal host toxicity. The first L-nucleoside ( -L-dT) was syn-

thesized by mejkal and orm in 1964 [42]; in the same year Ac-

ton, Ryan, and Goodman described -L-adenosine [244]. Related

ribonucleosides were reported by Shimizu in 1967 [245] and by

Hol and orm in 1969 [246]. The discovery of the antiviral activ-

ity of 3TC, which is more active and less toxic than its D-

counterpart, attracted considerable interest in the synthesis and the

pharmacological activity of L-nucleosides [247-253]. Their antivi-

ral activity is comparable and even greater than that of their D-

counterparts. Better toxicological profiles and a greater metabolic

stability were observed in several cases. L-Nucleosides and their

analogs have become effective drugs for the treatment of viral dis-

eases. A number of them, such as lamivudine (3TC) and FTC are

commercialized; others like L-dT and L-FMAU are expected to get

approval by the FDA [248-250]. In the following, the synthesis of a

number of 7-deazapurine -L-2’-deoxyribonucleosides is described.

Considering the identical chemical properties of L- and D-

nucleosides and their precursors in a non-chiral environment, the

protocols developed for the 7-deazapurine D-nucleoside synthesis

can be employed for the preparation of the corresponding L-

enantiomers. Instead of the corresponding halogenose 7, 2-deoxy-

3,5-di-O-(p-toluoyl)- -L-erythro-pentofuranosyl chloride (8) was

used as sugar component. The L-sugar 8 was prepared according to

the procedure described for the corresponding D-enantiomer 7 [41,

254]. Solid-liquid nucleobase anion glycosylation [33, 34, 38] of 7-

deazapurines 33a,d with the halogenose 8 (TDA-1/KOH/MeCN)

afforded the toluoyl-protected -L-nucleosides 240a,d stereoselec-

tively in 68-89% yield (Scheme 60). Deprotection of compound

240d under concomitant nucleophilic displacement of the chloro

substituent (aq. NH3/dioxane, 80°C) gave -L-2’-deoxytubercidin

(242a). Compound 240d was treated with methanolic ammonia to

yield the 6-chloro intermediate 241d, which was later converted to

-L-2’-deoxy-7-iodotubercidin (242d) in aq. NH3/dioxane (120°C)

[255].

Also, a number of 6,7-disubstituted 2-amino-7-deazapurine -

L-2’-deoxyribonucleosides were prepared. The glycosylation of the

2-amino-6-chloro-7-deazapurines 27a,b [53, 256] with L-

halogenose 8 performed under solid-liquid conditions gave the -L-

nucleosides 243a (85%) or 243b (66%) exclusively (Scheme 61).

The intermediates 243a,b were deprotected (methanolic ammonia)

affording nucleosides 244a,b.

The protected nucleosides 243a,b were also employed in vari-

ous nucleophilic displacement reactions [255] (Scheme 61). Re-

moval of the toluoyl protecting groups and displacement of the 6-

chloro substituent occurred upon treatment of 243a,b with 25% aq.

NH3 in a steel vessel furnishing the 2,6-diamino nucleosides

245a,b. Selective deamination of compounds 245a,b with sodium

nitrite in AcOH/H2O (V/V, 1:5) gave the 7-deazaisoguanine deriva-

tives 246a,b (60-70% yield). Compounds 243a,b were also con-

verted to the 6-methoxy nucleosides 247a,b with 0.5 M

NaOMe/MeOH (reflux conditions). The 7-deaza- -L-2’-

deoxyguanosines 248a,b were obtained from 247a,b by nucleo-

philic methoxy/hydroxy group displacement in refluxing 2 N

NaOH. The 6-thio compound 249 was prepared from 244a using

thiourea (Scheme 62).

Structural and conformational parameters of a few L-

nucleosides were obtained in the solid state from single-crystal X-

ray analyses. The X-ray structure of the L-enantiomer 2’-deoxy-7-

iodotubercidin (242d) is shown in Fig. (30) [255]. The conforma-

N

N NH

Cl

MeCN, KOH, TDA-1

N

N

Cl

NO

+ OTol

OTol

Cl

O

OTol

OTol

a: 68%

d: 89%

R

R

8

a: R = H; d: R = I

33a,d

240a: R = H

d: R = I

N

N

NH2

N

O

OH

OH

aq. NH3,

dioxane

NH3,

MeOH

87%

242a,d241d

R

N

N

Cl

N

O

OH

OH

I

240d 240a

aq. NH3,

dioxane

81%40%

Scheme 60.


tion around the glycosyl bond was found to be anti with the torsion

angle (O4’-C1’-N9-C4) of 147.1°, and the sugar moiety adopts

the S-conformation (3E; P = 197° and m = 32.7°).

The -L-configuration was deduced from the CD spectra meas-

ured for both, the 7-deazapurine L-nucleosides and the correspond-

ing D-enantiomers. Typical spectra are shown in Fig. (31a,b). By

comparing the CD spectra of the -L- and -D-nucleosides, mirror

images confirmed the enantiomeric character. The -L-nucleosides

show a positive lobe while a negative lobe is formed by the -D-

enantiomers.

6. SYNTHESIS OF PYRROLO[2,3-d]PYRIMIDINES WITH

UNUSUAL GLYCOSYLATION SITES

In the early days of 7-deazapurine 2’-deoxyribonucleoside syn-

thesis, the major research focus was directed towards the develop-

N

N NH

Cl

H2N

N

N

Cl

H2N N

O

+OTol

OTol

Cl

O

OTol

OTol

N

N

Cl

H2N N

O

OH

OH

R

R

R

8

a: R = H; b: R = Cl

27a,b

243a,b

244a,b

N

N

NH2

H2N N

O

OH

OH

245a,b 247a,b

R

246a,b

N

N

OMe

H2N N

O

OH

OH

R

HN

N

NH2

O N

O

OH

OH

R

248a,b

HN

N

O

H2N N

O

OH

OH

R

aq. NH3,

dioxane

NaOMe,

MeOH

AcOH/H2O,

NaNO2, rt2N NaOH,

reflux

TDA-1, KOH,

MeCN

NH3/MeOH, rt

a: 85%

b: 66%

a: 88%

b: 90%

a: 71%

b: 91%

a: 90%

b: 80%

a: 81%

b: 87%

a: 70%

b: 60%

Scheme 61.

HN

N

S

H2N N

O

OH

OH

N

N

Cl

H2N N

O

OH

OH

(NH2)2CS, EtOH,

reflux

244a 249

85%

Scheme 62.


ment of a convenient glycosylation protocol allowing glycosylation

at the desired position-9 (pyrrole nitrogen) of the 7-deazapurine

moiety (see also section 2). However, 7-deazapurine 2’-deoxyribo-

nucleosides with unusual glycosylation sites, e.g. with nitrogen-1,

carbon-8 or carbon-7 as glycosylation position, show interesting

properties.

6.1. 7-Deazapurine Nucleosides with Carbon-8 as Glycosylation

Position

Because of the weak nucleophilicity of the pyrrole nitrogen of

7-deazapurines, nucleosides with unusual glycosylation positions

are readily formed (see also section 2). Even C-nucleosides can be

generated selectively in the presence of a protected sugar moiety

with Friedel-Crafts catalysts such as SnCl4 [257]. This protocol,

which is commonly named Vorbrüggen glycosylation, has been

applied to the synthesis of 7-deazaguanine ribonucleosides with

carbon-8 or carbon-7 as glycosylation position. Corresponding 2’-

deoxyribonucleosides were synthesized by Barton deoxygenation

(see also section 3.3).

Glycosylation of the unprotected 7-deazaguanine base (250a)

with 1-O-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose (251) in ni-

tromethane in the presence of SnCl4 afforded the benzoyl protected

C8-ribonucleoside 252 (Scheme 63) [257]. Compound 252 was

deprotected with saturated methanolic ammonia to give the C8-

glycosylated 7-deazaguanine ribonucleoside 253 (78% yield).

The same authors evaluated the reactivity of 8-methyl-7-

deazaguanine (250b) with the protected sugar 251 under the condi-

tions mentioned above (nitromethane, SnCl4). In this case position-

8 is blocked by the methyl group. Now, electrophilic C-

glycosylation occurred at position-7 ( 254); however the yield

was lower (47%) compared to glycosylation at position-8 (56%)

Fig (30). Perspective view showing the displacement ellipsoids obtained

from the single-crystal X-ray analyses of compound 242d [255].

Fig (31). CD spectra of L-7-deaza-2’-deoxyguanosines (248a,b), L-2’-deoxytubercidin (242a) and their corresponding D-counterparts (12a,b and 14a). Spec-

tra were measured in MeOH with nucleoside concentrations of 4.1 10-5

(a) and 9.5 10-5

mol/L (b) [255].

O

BzO

BzO

252

HN

NH2N N

O

H

O

BzO

BzO

OBz

OAc

NH

N

H2N

N

O

OBz

nitromethane, SnCl4,

60°C, 3h

O

HO

HO

253

NH

N

H2N

N

O

OH

H HNH3/MeOH

56%78%

250a

251

Scheme 63.


employing 7-deazaguanine (250a) as nucleobase. Deprotection

(NH3/MeOH) of the protected intermediate 254 afforded the free

C7-ribonucleoside 255 in 48% yield (Scheme 64). The authors con-

cluded that electrophilic C-glycosylation in nitromethan using

SnCl4 as catalyst occurs preferentially at position-8, unless that

position is blocked. In that case, glycosylation proceeds at position-

7 [257].

The synthesis of the corresponding isobutyrylated 2’-

deoxyribonucleoside 260 employing ribonucleoside 253 as starting

material was achieved by Barton deoxygenation [117, 258]. First,

the amino group of 253 was protected with an isobutyryl residue

employing the protocol of transient protection ( 256; 72% yield)

(Scheme 65) [259]. Compound 256 was treated with Markiewicz’s

reagent [118] to give the silyl derivative 257 (57% yield). Reaction

O

BzO

BzO

254

HN

NH2N N

O

H

HN

NH2N N

O

OBz

251, nitromethane,

SnCl4, 60°C, 3h

H

NH3/MeOH

47% 48%

250b

CH3

CH3

O

HO

HO

255

HN

NH2N N

O

OH

H

CH3

Scheme 64.

O

HO

HO

253

NH

N

H2N

N

O

OH

H

O

HO

HO

256

NH

N

i-BuHN

N

O

OH

H

(i-Bu)2O, pyridine,

rt, 3h

O

O

O

257

NH

N

i-BuHN

N

O

OH

H

Si

O

Si

i-Pr i-Pr

i-Pr

i-Pr

(i-Pr)2ClSiOSi(i-Pr)2Cl,

pyridine, rt, 12h

O

O

O

258a: R = H (48%)

b: R = C(S)OPh (10%)

NH

N

i-BuHN

N

O

OCOPh

Si

O

Si

i-Pr i-Pr

i-Pr

i-Pr

R

S

PhOC(S)Cl, MeCN,

rt, 12h

O

O

O

259

NH

N

i-BuHN

N

O

H

Si

O

Si

i-Pr i-Pr

i-Pr

i-Pr

258a: (n-Bu)3SnH,

AIBN, toluene,

60°C, 4h

257

O

HO

HO

260

NH

N

i-BuHN

N

O

H

0.1N TBAF/THF,

rt, 3h

O

HO

DMTO

261

NH

N

i-BuHN

N

O

H

DMT-Cl, pyridine,

rt, 3h

O

O

DMTO

262

NH

N

i-BuHN

N

O

H

P

NCCH2CH2O N(i-Pr)2

(i-Pr)2NP(Cl)O(CH2)2CN,

CH2Cl2, rt, 20 min

72% 57%

90% 82%

72% 78%

260

Scheme 65.


of the silylated 257 with phenoxythiocarbonyl chloride in MeCN

furnished the 2’-O-phenoxythiocarbonyl derivative 258a (48%)

together with the bisphenoxythiocarbonyl compound 258b (10%) as

by-product. Reductive cleavage of 258a with tri-n-butyltin(IV)

hydride in toluene in the presence of AIBN yielded the 2’-deoxy

derivative 259 (90%). Desilylation with 0.1 N TBAF in anhydrous

THF gave the isobutyrylated 2’-deoxyribonucleoside 260 (82%).

However, the unprotected nucleoside was difficult to isolate due to

its unfavourable chromatographic properties. In order to prepare a

phosphoramidite building block of 260 which can be employed in

solid-phase oligonucleotide synthesis, the DMT group was intro-

duced at the 5’-hydroxyl group ( 261; 72%). The phosphoramid-

ite 262 was prepared under standard conditions from compound 261

(78% yield). For application of 262 in oligonucleotide synthesis and

properties of corresponding oligonucleotides, we refer to reference

[258].

6.2. 7-Deazapurine Nucleosides with Nitrogen-1 as Glycosyla-

tion Site

6.2.1. Fluorescent Pyrrolo-C 2’-Deoxyribonucleosides and

Analogs Thereof

Pyrrolo-dC (263a) contains the same 7-deazapurine (pyr-

rolo[2,3-d]pyrimidine) moiety as the fluorescent 7-deaza-2’-

deoxyisoinosine (37), but employing nitrogen-1 as glycosylation

position (Fig. 32). Also, pyrrolo-dC (263a), the corresponding ribo-

nucleoside pyrrolo-C (263b), and its 6-alkylated or alkynylated

derivatives (263c-j) develop significant fluorescence. This section

deals with the synthesis of pyrrolo-dC derivatives comprising sim-

ple alkyl or alkynyl side chains and studies of their fluorescence

properties, whereas pyrrolo-dC derivatives with complex side

chains that are prone to form additional hydrogen bonds in duplex

or triplex DNA are addressed in section 6.2.2. Due to the common

HN

NO

O

HO

N

HO

37

N

N

O

O

HO

HO

263a: R = H

b: R = OH

N

N

O

O

HO

HO

c: R = CH3

R

HN HN

R

d: R = (CH2)3

e: R = (CH2)4

f: R = (CH2)3 CH3

g: R = (CH2)5 CH3

h: R = CH2NHCOCF3

Phj: R =

i: R = CH2OCH3

263c-j

(3)

(1)

(7)(6)

(4a)

(systematic numbering)

purine numbering

1

3

98

5

Fig (32).

I

O

O

N

N

O

NH2

O

N

N

AcN

O

(Ph3P)PdCl2, CuI, Et3N,

DMF, N2, 60°C

265a: R = Si(CH3)3

R

f: R = (CH2)3

Si

O

Si

i-Pri-Pr

i-Pr

i-Pr

C

O

O

N

N

O

NH2

O

Si

O

Si

i-Pri-Pr

i-Pr

i-Pr

HC C R,C R

Ac2O

C

O

O

N

N

O

NHAc

O

Si

O

Si

i-Pri-Pr

i-Pr

i-Pr

C R

264

CH3

266a: R = Si(CH3)3

f: R = (CH2)3CH3

O

O

O

Si

O

Si

i-Pri-Pr

i-Pr

i-Pr

267a: R = H

f: R = (CH2)3CH3

N

N

HN

O

R

O

HO

HO

263a: R = H

f: R = (CH2)3CH3

CuI, DMF,

N2, 120°C

1) TBAF

2) NH4OH

266a,f

a: 90%

f: 83%

a: 78% over 2 steps

f: 81.5% over 2 steps

a: 75%

f: 75%

Scheme 66.


application of the systematic numbering in reports on pyrrolo-C

nucleosides, we employed this numbering throughout sections

6.2.1. and 6.2.2.

The synthesis of pyrrolo-dC (263a) using silylated 2’-deoxy-5-

iodocytidine (264) as starting material was first reported by

Ohtsuka and co-workers [260]. Introduction of the silylated ethynyl

side chain was achieved by cross-coupling in DMF in the presence

of (Ph3P)PdCl2, CuI and EtN3 to give the protected intermediate

265a in 90% yield. Next, the amino group was protected by acetyla-

tion ( 266a). Ring closure was performed in DMF with CuI, and

the silylated pyrrolo-dC derivative 267a was obtained in 78% over

two steps. Desilylation with TBAF followed by NH4OH treatment

afforded the unsubstituted pyrrolo-dC 2’-deoxyribonucleoside 263a

(75% yield). The 6-butyl derivative of pyrrolo-dC 263f was pre-

pared following the same procedure as shown in Scheme 66 [260].

Later, Gamper et al. obtained pyrrolo-dC (263a) via the

furano[2,3-d]pyrimidine intermediate 269a by oxygen nitrogen

exchange [261]. This route employs 2’-deoxy-5-ethynyluridine

(268a) as precursor [262, 263]. Cyclization of 268a was achieved

with copper iodide in the presence of Et3N in DMF to give the

furano[2,3-d]pyrimidine intermediate 269a in 83% yield. Treatment

of compound 269a with 30% aq. ammonia at room temperature

afforded the 7-deazapurine nucleoside 263a in high yield (95%)

(Scheme 67). On the contrary, it was demonstrated by others that no

oxygen nitrogen exchange takes place when a 5’,3’-di-acetylated

6-p-toluoyl furano[2,3-d]pyrimidine nucleoside was treated with

NH3 in methanol at room temperature for 20 h [264]. Under these

conditions, only the deprotected 6-p-toluoyl furano[2,3-

d]pyrimidine nucleoside was obtained.

Accordingly, a number of 6-alkylated or alkynylated pyrrolo-

dC analogs (263c-e) were prepared from their corresponding 5-

alkynylated 2’-deoxyuridine precursors (268c-e) as shown in

Scheme 68 [82, 265-267]. It should be noted that in some cases

already during Sonogashira cross-coupling, the formation of cy-

clized furano-pyrimidine nucleosides was reported [82, 267]. Al-

though in the context of pyrrolo-dC synthesis, furano-pyrimidine

nucleosides only function as intermediates, it is worthwhile to men-

tion that several analogs thereof show promising antiviral activities

[268, 269].

An alternative synthetic route makes use of the low nucleophil-

icity of the pyrrole nitrogen allowing the regioselective nucleobase

anion glycosylation at nitrogen-3 (pyrimidine moiety). This route

was exemplified on the ribonucleoside pyrrolo-C (263b) by our

laboratory and others (Scheme 69) [82, 270, 271], but was not ap-

plied to its 2’-deoxy derivative.

O

HO

HN

N

HO

O

O

O

HO

N

N

HO

O

O

O

HO

N

N

HO

HN

O

CuI, Et3N, DMF 30% aq. NH3, rt

83% 95%

268a 269a 263a

Scheme 67.

R

O

HO

HN

N

HO

O

O

O

HO

N

N

HO

O

O

O

HO

N

N

HO

HN

O

CuI, Et3N, MeOH,

reflux

25% aq. NH3,

rt or 50°C

268c: R =

R R

CH3

(CH2)3

(CH2)4

269c: R = CH3 (61% or 95%)

(CH2)3

(CH2)4

263c: R = CH3 (90% or 95%)

(CH2)3

(CH2)4

(90%)

(87%)

(92%)

(90%)

d: R =

e: R =

d: R =

e: R =

d: R =

e: R =

Scheme 68.

O

BzO

BzOO

BzO

N

N

BzO

HN

O

O

HO

N

N

HO

HN

O

BSA, TMSOTf,

80°C NaOMe/MeOH, rt

87% 81%

270

271 263b

OBz

OAc

HN

N NO

H

251

+

OBz OH

Scheme 69.


6-Methylpyrrolo-dC (263c) was also converted into its corre-

sponding phosphoramidite building block (Scheme 70) and em-

ployed in solid-phase oligonucleotide synthesis [266]. However, as

reported by Berry and co-workers, building block synthesis used

the furano-pyrimidine intermediate 269c as precursor and introduc-

tion of the DMT residue was performed first ( 272c; 87% yield).

In the next step, conversion of the DMT protected furano-

pyrimidine intermediate 272c into the 7-deazapurine pyrrolo-dC

nucleoside 273c was accomplished using saturated ammonia in

MeOH in a pressure bottle at 50°C (49% yield). Phosphitylation ((i-

Pr2)2POCH2CH2CN, 1H-tetrazole, CH2Cl2, rt) of 273c gave com-

pound 274c in 53% yield as outlined in Scheme 70.

Similar routes were chosen for the phosphoramidite building

block synthesis of compounds 274h-j [272-274]. However, the

O

HO

N

N

DMTO

HN

O

O

O

N

N

DMTO

HN

O

sat. NH3 in MeOH,

pressure bottle, 50°C

(i-Pr2N)2POCH2CH2CN,

1H-tetrazole, CH2Cl2,

rt, 4.5h

P

NCCH2CH2O N(i-Pr)2

O

HO

N

N

DMTO

O

O

DMT-Cl, pyridine,

CH2Cl2

87% 49%

53%

272c

273c

274c

O

HO

N

N

HO

O

O

269c

273c

Scheme 70.

O

HO

N

N

DMTO

HN

O

O

O

N

N

DMTO

HN

O

aq. NH3, MeOH,

55°C

i-Pr2NP(Cl)OCH2CH2CN,

Et3N, CH2Cl2, rt

R R

P

NCCH2CH2O N(i-Pr)2

O

HO

N

N

DMTO

O

O

269h: DMT-Cl,

pyridine, DMAP

O

HO

HN

N

R2O

O

O

R1

268h: R1 = CH2NHCOCF3, R2 = H

Ph, R2 = DMT275j: R1 =

O

HO

N

N

R2O

O

O

R

CuI, Et3N, MeOH,

reflux

275i: R1 = CH2OCH3, R2 = DMT

269h: R = CH2NHCOCF3, R2 = H (77%)

Ph, R2 = DMT272j: R =

272i: R = CH2OCH3, R2 = DMT

272h (84%)

272h-j

273h: R = CH2NHCOCF3 (50%)

Ph (78%)j: R =

i: R = CH2OCH3 (85%)

274h: R = CH2NHCOCF3

Ph (80%)j: R =

i: R = CH2OCH3

NH

CF3

O

Scheme 71.


DMT residue was introduced at different stages for 274h and 274i,j

as demonstrated in Scheme 71. The first method employs the

trifluoroacetyl protected 6-propargyl derivative of 2’-deoxyuridine

268h as precursor [272]. First, ring closure towards the furano-

pyrimidine intermediate 269h was performed (77%), then the 5’-

hydroxyl group was protected with the DMT residue ( 272h;

84%). The second method utilizes the DMT-protected 5-

functionalized 2’-deoxyuridines 275i,j as precursors [273, 274].

Cyclization was performed on the DMT compounds 275i,j to afford

the furano[2,3-d]pyrimidine nucleosides 272i,j. Next, the oxygen to

nitrogen exchange was performed on 272h-j by ammonia treatment

yielding 273h-j. Conversion into the phosphoramidite building

blocks 274h-j was achieved under standard conditions (i-

Pr2P(Cl)OCH2CH2CN, Et3N, CH2Cl2, rt). Compounds 274h-j were

employed in solid-phase oligonucleotide synthesis, and the proper-

ties of 263i,j as constituents of oligonucleotides were investigated.

Oligonucleotides containing 263h were labelled with pyrene on the

oligonucleotide level after removal of the trifluoroacetyl protecting

group and utilized as molecular beacons [272].

A variation of the phosphoramidite building block synthesis of

the 6-phenyl derivative of pyrrolo-dC (274j) comprises acetylated

2’-deoxy-5-phenylethynyluridine (276) as starting material

(Scheme 72) [273]. Cyclization to the acetylated furano[2,3-

d]pyrimidine compound 277 was performed under Ag+-catalyzed

conditions (AgNO3, acetone, rt) as reported by Agrofoglio [275].

Deacetylation and oxygen to nitrogen exchange were performed in

one step followed by dimethoxytritylation to afford the DMT-

protected pyrrolo-dC compound 273j in 68% over two steps. As

described above, 273j was converted into phosphoramidite 274j.

Alternatively, conversion of furano[2,3-d]pyrimidine nucleo-

sides into their corresponding pyrrolo-dC derivatives can also be

achieved on oligonucleotide level by ammonia treatment (standard

oligonucleotide deprotection conditions) [261, 265, 266, 276, 277].

In this context, phosphoramidite building blocks of the furano[2,3-

d]pyrimidine nucleoside 278a,c,e,g,k,l were synthesized first as

shown in Scheme 73. This protocol was chosen for the synthesis of

oligonucleotides incorporating nucleosides 263a,c,e,g. Two routes

1) aq. NH3, MeOH,

55°C

2) DMT-Cl, pyridinei-Pr2NP(Cl)OCH2CH2CN,

Et3N, CH2Cl2, rt

O

AcO

N

N

AcO

O

O

Ph

O

AcO

HN

N

AcO

O

O

AgNO3, acetone,

rt, 24h

274j273j

Ph

75% 68% over 2 steps 80%

276 277

Scheme 72.

R

O

HO

HN

N

DMTO

O

O

O

HO

N

N

DMTO

O

O

O

O

N

N

DMTO

O

O

CuI, Et3N,

MeOH,

reflux


i-Pr2EtN, CH2Cl2, rt

R R

(CH2)4

(CH2)5

P

NCCH2CH2O N(i-Pr)2

CH3

CH3

O

HO

N

N

HO

O

O

R

269a: R = H

c: R = CH3

e: R = (CH2)4

275e: R =

g: R =

278a: R = H

c: R = CH3

e: R = (CH2)4

g: R = (CH2)5

CH3

272a: R = H

c: R = CH3

e: R = (CH2)4

g: R = (CH2)5

DMT-Cl,

pyridine

(CH2)2NPhthk: R =

(CH2)3NPhthl: R =

(CH2)2NPhthk: R =

(CH2)3NPhthl: R =

(CH2)2NPhthk: R =

(CH2)3NPhthl: R =

Scheme 73.


were employed for the preparation of the DMT compounds

272a,c,e,g,k,l. The first method starts with the dimethoxytritylation

of the furano[2,3-d]pyrimidine nucleosides 269a,c,e yielding the

DMT protected compounds 272a,c,e. The second method begins

with the cyclization of the already DMT-protected alkylated or

alkynylated 2’-deoxyuridine analogs 275e,g,k,l affording the DMT-

protected furano[2,3-d]pyrimidine nucleosides 272e,g,k,l.

Phosphitylation was performed under standard conditions. The

phosphoramidites 278a,c,e,g,k,l were employed in solid-phase oli-

gonucleotides synthesis [261, 265, 266, 276, 277]. During deprotec-

tion (25% aq. NH3, 60°C, 14 h) of the oligonucleotides, the

furano[2,3-d]pyrimidine residues derived from 278a,c,e,g were

converted into their corresponding 7-deazapurine (pyrrolo[2,3-

d]pyrimidine) congeners as indicated in Scheme 74A [261, 265,

266, 277]. Deprotection of some oligonucleotides containing

furano[2,3-d]pyrimidine moieties derived from 278c,k,l was per-

formed in the presence of 30% aq. methylamine followed by recy-

clization with DOWEX ion-exchange resin (H+ form) (Scheme

74B) [276]. In this case, oxygen-7 of the furano[2,3-d]pyrimidine

moiety was replaced by an N-methyl group resulting in N7-

methylated 6-substitued pyrrolo-dC analogs as components of oli-

gonucleotides.

Pyrrolo-dC (263a), the corresponding ribonucleoside pyrrolo-C

(263b), and its 6-alkylated or alkynylated derivatives (263c-j) de-

velop significant fluorescence. Fluorescence spectra of 6-

hexynylpyrrolo-dC (263e) show an excitation maximum at 340 nm

with an emission at 466 nm (stoke shift of 126 nm), and the fluo-

rescence quantum yield ( ) of 263e in double distilled water was

determined to be 0.05 [265]. A representative emission and excita-

tion spectrum of 263e is shown in Fig. (33). Compared to the parent

ribonucleoside 263b, the introduction of a hexynyl side chain at

position-6 has almost no influence on the excitation maximum

(263b: 336 nm) and the quantum yield (263b: = 0.06). However,

the emission maximum of 263e is shifted to higher wavelengths

compared to 263b (450 nm).

Although pyrrolo-dC (263a) and its derivatives show signifi-

cant fluorescence, their extinction coefficients and quantum yields

are low when compared to fluorescent dyes like coumarin or

pyrene. In this context, our laboratory subjected 6-hexynylpyrrolo-

dC (263e) bearing a terminal triple bond to the copper(I)-catalyzed

Huisgen-Meldal-Sharpless “click” reaction (see also section 4.1.1)

and conjugated 263e to 3-azido-7-hydroxycoumarin (118) as shown

in Scheme 75 [265]. The pyrrolo-dC-coumarin conjugate 279 has

an excitation maximum at 350 nm with an emission at 476 nm

(stoke shift of 126 nm) at neutral pH (Fig. 34a) and an excitation

maximum at 392 nm with an emission at 476 nm at pH 8.5 (Fig.

34b). The fluorescence properties of coumarin derivatives are

strongly pH dependent, and at neutral pH the generation of the

O

O

N

N

O

O

O

O

O

N

N

O

HN

O

25% aq. NH3,

60°C, 14h

R R

DNA

DNA

DNA

DNA

CH3

R = H

R = (CH2)4

R = (CH2)5

R = CH3

O

O

N

N

O

O

O

O

O

N

N

O

N

O

R R

DNA

DNA

DNA

DNA

NH3R = (CH2)2

R = CH3

NH3R = (CH2)3

30% aq. MeNH2, Dowex

H+

A

B

Scheme 74.

Fig (33). The emission and excitation spectra of nucleoside 263e measured

at room temperature in double distilled water.


highly fluorescent phenolate anions is limited. At pH 7, the stoke

shifts of the 6-hexynylpyrrolo-dC nucleoside 263e and its click

derivative 279 are almost identical. However, the fluorescence

quantum yield of 279 was determined to be 0.18, which is signifi-

cantly higher than that of the parent nucleoside 263e ( = 0.05). On

the contrary, the closely related coumarin click conjugate of 2’-

deoxy-5-octa-1,7-diynyluridine (280; Scheme 75) reveals a quan-

tum yield of = 0.32 which is significantly higher than that of the

pyrrolo-dC click conjugate 279. From these findings, it was con-

cluded that the 7-deazapurine moiety of 279 quenches the fluores-

cence of the coumarin dye [265].

6.2.2. Pyrrolo-dC Analogs Forming Additional Hydrogen Bonds

Recent efforts have been dedicated to the development of novel

cytosine analogs which stabilize DNA duplexes through the forma-

tion of additional hydrogen bonds to the Hoogsteen binding sites of

guanine. These derivatives utilize either 9-aminoethoxy phenoxaz-

ine (“G-clamp”) [278, 279] or 6-substituted pyrrolo-C as their het-

erocyclic moiety [280, 281]. The work on phenoxazine nucleosides

goes back to a publication of Matteucci and co-workers reporting

for the first time on the synthesis of tricyclic phenoxazine deriva-

tives that are capable of base pairing [282]. Within the last years,

the extraordinary duplex stabilizing properties of the G-clamp com-

bined with its mismatch discrimination properties initialized the

syntheses of various closely related G-clamp analogs and their

building blocks for DNA, RNA or PNA [283-285]. Less work has

been dedicated to the development of 6-substituted pyrrolo-dC de-

rivatives which are also capable of forming additional hydrogen

bonds in duplex DNA. However, the extended hydrogen bonding

motif of 6-modified N-methylpyrrolo-dC nucleosides was used for

the recognition of the dC•dG base pair in triplex DNA [280, 281].

Two protocols have been used for the introduction of N-methyl

pyrrolo-dC nucleosides into oligonucleotides. The first one makes

use of furano[2,3-d]pyrimidine phosphoramidite building blocks as

demonstrated in Schemes 73 and 74, and the replacement of oxy-

gen-7 by the N-methyl group was accomplished on oligonucleotide

level. The second protocol utilizes N-methyl pyrrolo-dC phos-

phoramidite building blocks for solid-phase oligonucleotide synthe-

sis.

For the synthesis of the furano[2,3-d]pyrimidine phosphoramid-

ite building blocks 284a-c with m-trifluoroacetamido-, ureido-, and

O

HO

N

HO

N

O

HN

263e

N3

O OHO

118

O

O

N

N

N

OH

O

HO

N

HO

N

O

HN

279

CuSO4 5 H2O

Na-ascorbate

THF:H2O:t-BuOH

+85%

O

O

N

N

N

OH

O

HO

N

HO

HN

O

O

280

Scheme 75.

Fig (34). The emission and excitation spectra of the pyrrolo-dC coumarin conjugate 279 measured (a) in water (pH 7.0) and (b) in 0.1 M Tris-HCl buffer (pH

8.5).


acetamido-phenyl side chain modifications at position-6 of the het-

erocyclic moiety, the DMT protected 2’-deoxyuridine derivatives

281a-c were used as starting material. Compounds 281a-c were

constructed by Sonogashira cross-coupling [280] and were cyclized

using CuI and Et3N in MeOH to yield the DMT-protected

furano[2,3-d]pyrimidine nucleosides 282a-c in 69-96% yield. The

aniline moiety of 282a was further protected using ethyl

trifluoroacetate ( 283a) as indicated by Scheme 76. Phosphityla-

tion of 282b,c and 283a under standard conditions furnished the

phosphoramidites 284a-c in 64-69% yield. Conversion of the

furano[2,3-d]pyrimidine moieties to the N-methyl pyrrolo[2,3-

d]pyrimidine derivatives was achieved with aq. methylamine on the

oligonucleotide level as described in section 6.2.1 and illustrated in

Scheme 74B. However, this protocol was encountered with difficul-

ties as it was found that, the re-cyclization of the N-methyl 7-

deazapurine moiety was incomplete in some cases (identified by

HPLC analysis) [281].

The alternative strategy requires the synthesis of protected 2’-

deoxy-5-iodo-4N-methylcytidine (287) as starting material [281].

The synthesis route is outlined in Scheme 77 and uses 5’-DMT

protected 2’-deoxy-5-iodouridine (285) as precursor. Then, the 3’-

hydroxyl group was acetylated ( 286). For the conversion of 286

into the target compound 287, the 4-carbonyl position was activated

first using N-methylimidazole (NMI) and POCl3 in pyridine. After

the introduction of methylamine and deacetylation, the DMT com-

pound 2’-deoxy-5-iodo-4N-methylcytidine 287 was obtained in

88% yield. Several side chains were introduced via the Pd-

catalyzed Sonogashira cross-coupling reaction employing different

phenyl acetylene residues (288a-d). Cyclization was achieved with

CuI and Et3N in DMF to yield N-methyl pyrrolo-dC analogs with

phenyl (289a), acetamido (289b), ureido (289c) or phenylamino

(289d) modifications at position-6 (Scheme 78). The amino group

of 289d was further protected using ethyl trifluoroacetate ( 289e).

Conversion into the corresponding phosphoramidites was achieved

under standard conditions and gave 290a-c,e in 51-86% yield [281].

The 6-guanidinyl derivative 292 was obtained in 44% yield

from compound 289d using isothiourea (291) as guanidinylation

reagent (Scheme 79). Subsequent phosphitylation afforded phos-

phoramidite 293 in 47% yield. The building blocks 290a-c,e and

293 were incorporate into triplex forming oligonucleotides (TFOs)

and deprotected under standard conditions. The binding affinity and

selectivity for dC•dG was evaluated. For details, we refer to [281].

7. CONCLUSION AND OUTLOOK

As 7-deazapurines mimic the shape of purines ideally, the cor-

responding 2'-deoxyribonucleosides can replace canonical purine

constituents of DNA. Moreover, they are substrates or inhibitors of

various enzymes. A highly stable glycosylic bond and a rather inert

6-amino function make this class of modified nucleosides resistant

against nucleoside converting enzymes, such as nucleoside phos-

phorylase or adenosine deaminase.

O

HO

HN

N

DMTO

O

O

O

HO

N

N

DMTO

O

O

O

O

N

N

DMTO

O

O

CuI, Et3N,

MeOH, 80°C


i-Pr2EtN, THF, rt

P

NCCH2CH2ON(i-Pr)2

281a: R = H

b: R = COCH3

c: R = CONH2

NHR

NHR

NHR

282a: R = H (96%)

b: R = COCH3 (89%)

c: R = CONH2 (69%)

O

HO

N

N

DMTO

O

O

NHR

282a: CF3COOEt, DMAP,

Et3N, THF, 80-85°C

283a: R = COCF3 (35%)

a: R = COCF3 (64%)

b: R = COCH3 (69%)

c: R = CONH2 (69%)

284a-c

Scheme 76.


Initially, the preparation of 7-deazapurine 2’-deoxyribo-

nucleosides was encountered with difficulties, but after the devel-

opment of the nucleobase anion glycosylation protocol they became

easily accessible. The central key step of this protocol comprises

the formation of the nucleobase anion as highly reactive compo-

nent. Generation of the nucleobase anion can be achieved (i) under

liquid-liquid conditions, (ii) under solid-liquid conditions or (iii) by

the sodium salt glycosylation. The second important component of

the nucleobase anion glycosylation is the halogenose. By employ-

ing one among the different halogenose derivatives, the -D or -L

enantiomers of 7-deazapurine 2’-deoxyribonucleosides, 7-

deazapurine 2’-deoxy-2’-fluoroarabinonucleosides or 7-deazapurine

2’,3’-dideoxyribonucleosides can be prepared. Up to now, a broad

diversity of 7-deazapurine nucleosides has been synthesized using

one of the various glycosylation protocols. Alternatively, 7-

deazapurine 2’-deoxyribonucleosides can also be obtained from

their corresponding ribonucleosides by Barton-McCombie deoxy-

genation. Nucleophilic substitution reactions were carried out on

central intermidiates and led to various 7-deazapurine nucleosides

related to 2’-deoxyadensoine, 2’-deoxyguanosine or 2’-

deoxyinosine.

As position-7 of 7-deazapurine nucleosides points towards the

major groove of DNA, this site is an ideal position to introduce

functionalities into DNA. Regioselective halogenation reactions on

the various 7-deazapurine nucleosides have been performed, and it

was found that halogen substituents introduced at position-7 greatly

O

HO

HN

N

DMTO

O

OAc2O, pyridine,

0°C-rt, 3h

285

I

O

AcO

HN

N

DMTO

O

O

286

I

O

HO

N

N

DMTO

NH

O

287

I1) POCl3, NMI,

pyridine, 0°C-rt, 1h

2) aq. MeNH2,

0°C-rt, 16h

97% 88%

288a-d

alkyne, Pd(PPh3)4,

CuI, Et3N, DMF,

dark, rt

Scheme 77.

O

HO

N

N

DMTO

N

O

O

O

N

N

DMTO

N

O

CuI, Et3N, DMF,

dark, 125°C

289a-c,e:

i-Pr2NP(Cl)O(CH2)2CN,

i-Pr2EtN, CH2Cl2 or THF

or THF-DMF, rt

P

NCCH2CH2O N(i-Pr)2

R R

290a: R = H (66%)

b: R = NHCOCH3 (86%)

c: R = NHCONH2 (51%)

289a: R = H (71%)

b: R = NHCOCH3

c: R = NHCONH2

d: R = NH2 (80%)

e: R = NHCOCF3 (65%)

CF3CO2Et, DMAP, Et3N,

CH2Cl2

e: R = NHCOCF3 (70%)

O

HO

N

N

DMTO

NH

O

R

288a: R = H (90%)

b: R = NHCOCH3

c: R = NHCONH2

d: R = NH2 (95%)

Scheme 78.

O

HO

N

N

DMTO

N

O

O

O

N

N

DMTO

N

O

291, pyridine,

CH2Cl2, reflux, 2d

i-Pr2NP(Cl)O(CH2)2CN,

i-Pr2EtN, CH2Cl2, rt, 2h

P

NCCH2CH2O N(i-Pr)2

NH

293

289d 292

O

HO

N

N

DMTO

N

O

NH2

RN

NHR

R = CO2(CH2)2CN

NH

RN

NHR

44% 47%

NCO N

H

O

N O

S O

CN

291

Scheme 79.


increase duplex stability. An even better stabilization was observed

when the halogen substituents are replaced by alkynyl residues. The

strongly stabilizing effect on DNA makes 7-deazapurines good

candidates for primers or probes used in DNA diagnostics, sequenc-

ing or for antisense technology. Also, 7-deazapurine nucleosides

substituted with side chains carrying terminal triple bonds are ad-

vantageous for further functionalization employing the protocol of

the copper(I)-catalyzed Huisgen-Meldal-Sharpless “click” reaction.

“Click” reactions on 7-alkynylated 7-deazapurine 2’-

deoxyribonucleosides have been performed on nucleoside, nucleo-

tide as well as on oligonucleotide level and a broad range of azido

reporter groups have been utilized for labelling. Recently, the

“click” reaction has been used to crosslink 7-deazapurine 2’-

deoxyribonucleosides and oligonucleotides [149, 178].

The assembly of nucleosides and oligonucleotides to su-

pramolecular devices is another promising topic. Since 7-

deazapurines 2’-deoxyribonucleosides are very robust against alka-

line and acidic conditions, stable supramolecular structures can be

formed which might show advantages over the assemblies built up

by purine systems. As an example, aggregates of oligonucleotide

294 incorporating 7-bromo-7-deaza-2’-deoxyisoguanosine (36c;

Br7c

7iGd) have been shown to form a tetraplex in the presence of

Na+ (Fig. 35a) and Rb

+ (Fig. 35b), while a pentaplex is generated in

the presence of Cs+

(Fig. 35c) [286, 287]. Possible structures of

quadruplexes or pentaplexes are shown in Fig. (35d,e).

A variety of pyrrolo[2,3-d]pyrimidines develop antitumor activ-

ity. One of the recent prominent examples is Pemetrexed (Alimta®;

295), a folate antimetabolite which was developed by E. C. Taylor

[289] and brought into the market by the pharmaceutical company

Lilly (Fig. 36). Its antitumor activity is based on the inhibition of

enzymes acting in purine and pyrimidine synthesis. In that respect,

it can be expected that 7-dezapurine nucleosides possess a tremen-

dous potential to be used as anticancer or antiviral agents [208].

HN

N NH

O

H2N

295

NH

O

COOH

COOH

Pemetrexed, Alimta

Fig (36).

Moreover, modified pyrrolo[2,3-d]pyrimidine 2’-

deoxyribonucleosides and oligonucleotides will be applicable in

new areas of chemistry, physics, and biology, including nanotech-

nology and nanoelectronics. The use of DNA as a building block

for nanoelectronic sensors and devices due to its efficient hole-

conducting properties is currently under investigation. Recently, it

was reported that the charge-transfer efficiency of DNA can be

efficiently increased when 7-deaza-2’-deoxyadenosine is used as a

substitute of 2’-deoxyadenosine [290].

ACKNOWLEDGMENTS

We thank Mr. Ping Ding, Mr. Suresh S. Pujari, Mr. Sachin A.

Ingale and Dr. Peter Leonard for reading the manuscript and for

helpful comments. Financial support by the Bundesministerium für

Bildung und Forschung (BMBF) and ChemBiotech (Germany) is

gratefully acknowledged. We thank all people whose work is de-

scribed in this review.

REFERENCES

[1] Suhadolnik, R. J. Nucleoside as Biological Probes, Wiley-Interscience: New

York, 1979; pp. 158-169.

[2] Ranasinghe, R. T.; Brown, T. Fluorescence based strategies for genetic

analysis. Chem. Commun., 2005, 5487-5502.

[3] Suhadolnik, R. J. Nucleoside Antibiotics, Wiley-Interscience: New York,

1970.

[4] Martin, J. C. Nucleotide Analogues As Antiviral Agents, American Chemical

Society: Washington, 1989.

[5] Ritch, P. S.; Glazer, R. I. In: Developments in Cancer Chemotherapy; Glazer,

R. I., Ed.; CRC Press: Boca Raton, Florida, 1984.

[6] Seela, F.; Winkeler, H.-D.; J. Ott; Tran-Thi, Q.-H.; Hasselmann, D.; Franzen,

D.; Bussman, W. In: Nucleosides, Nucleotides, and their Biological

Applications; Rideout, J. L.; Henry, D. W.; III, L. M. B., Eds.; Academic

Press: New York, 1982.

[7] Kasai, H.; Ohashi, Z.; Harada, F.; Nishimura, S.; Oppenheimer, N. J.; Crain,

P. F.; Liehr, J. G.; von Minden, D. L.; McCloskey, J. A. Structure of

the modified nucleoside Q isolated from Escherichia coli transfer

ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-

deazaguanosine. Biochemistry, 1975, 14(19), 4198-4208.

[8] Naruto, S.; Uno, H.; Tanaka, A.; Kotani, H.; Takase, Y. Kanagawamicin, a

new aminonucleoside analog antibiotic from actinoplanes kanagawaensis.

Heterocyles, 1983, 20(1), 27-32.

[9] Kazlauskas, R.; Murphy, P. T.; Wells, R. J.; Baird-Lambert, J. A.; Jamieson,

D. D. Halogenated pyrrolo[2,3-d]pyrimidine nucleosides from marine

organisms. Aust. J. Chem., 1983, 36, 165-170.

[10] Kato, Y.; Fusetani, N.; Matsunaga, S.; Hashimoto, K. Bioactive marine

metabolites IX. Mycalisines A and B, novel nucleosides which inhibit cell

division of fertilized starfish eggs, from the marine sponge mycale sp.

Tetrahedron Lett., 1985, 26(29), 3483-3486.

[11] Seela, F.; Tran-Thi, Q.-H.; Franzen, D. Poly(7-deazaguanylic acid), the

homopolynucleotide of the parent nucleoside of queuosine. Biochemistry,

1982, 21(18), 4338-4343.

[12] Seela, F.; Peng, X. Base-Modified Oligodeoxyribonucleotides: Using

Pyrrolo[2,3-d] pyrimidines to Replace Purines. In: Current Protocols in

N

N

N

N

H

H

O H

N

N

N

NH

H

O

H

NN

NN

H

H

O

H

N

N

N

NH

H

O

H

N

NN

N

H

H

O

HN

N

N

O NH

H

N

NN

O

N

H

H

N

N

N

ON

N

H

N

NN

O

N

H

H

H

H

H

H

Cs+

Na+

d) e)

Br

Br

Br

Br Br

Br

Br

Br

Br

Fig (35). Ion-exchange HPLC elution profiles of oligomer 5’-d(T2Br7c

7iG6T2) (294) at 30°C in the presence of Na

+ (a), Rb

+ (b) and Cs

+ (c), conditions see

[286, 288]; (d) proposed structure for the tetraplex and (e) for the pentaplex.


Nucleic Acid Chemistry; Harkins, E. W., Ed. John Wiley & Sons: 2005; Vol.

1, pp. 4.25.1-4.25.25.

[13] Tavale, S. S.; Sobell, H. M. Crystal and molecular structure of 8-

bromoguanosine and 8-bromoadenosine, two purine nucleosides in the syn

conformation. J. Mol. Biol., 1970, 48(1), 109-123.

[14] Kanaya, E. N.; Howard, F. B.; Frazier, J.; Miles, H. T. Poly(8-

bromodeoxyadenylic acid): properties of the polymer and contrast with the

ribopolynucleotide analogue. Biochemistry, 1984, 23(18), 4219-4225.

[15] Sugiyama, H.; Kawai, K.; Matsunaga, A.; Fujimoto, K.; Saito, I.; Robinson,

H.; Wang, A. H.-J. Synthesis, structure and thermodynamic properties of 8-

methylguanine-containing oligonucleotides: Z-DNA under physiological salt

conditions. Nucleic Acids Res., 1996, 24(7), 1272-1278.

[16] Seela, F.; Röling, A. 7-Deazapurine containing DNA: efficiency of c7GdTP,

c7AdTP and c

7ldTP incorporation during PCR-amplification and protection

from endodeoxyribonuclease hydrolysis. Nucleic Acids Res., 1992, 20(1), 55-

61.

[17] Seela, F.; Röling, A. DNA-fragments resistant to endodeoxyribonuclease

hydrolysis PCR-amplification using 7-deaza-2 -deoxyguanosine triphosphate

in place of dGTP. Nucleosides Nucleotides, 1991, 10(1), 715-717.

[18] Seela, F.; Feiling, E.; Gross, J.; Hillenkamp, F.; Ramzaeva, N.; Rosemeyer,

H.; Zulauf, M. Fluorescent DNA: the development of 7-deazapurine

nucleoside triphosphates applicable for sequencing at the single molecule

level. J. Biotechnol., 2001, 86(3), 269-279.

[19] Mizusawa, S.; Nishimura, S.; Seela, F. Improvement of the dideoxy chain

termination method of DNA sequencing by use of deoxy-7-deazaguanosine

triphosphate in place of dGTP. Nucleic Acids Res., 1986, 14(3), 1319-1324.

[20] Barr, P. J.; Thayer, R. M.; Laybourn, P.; Najarian, R. C.; Seela, F.; Tolan, D.

R. 7-Deaza-2'-deoxyguanosine-5'-triphosphate: enhanced resolution in M13

dideoxy Sequencing. BioTechniques, 1986, 4(5), 428-432.

[21] Prober, J. M.; Trainor, G. L.; Dam, R. J.; Hobbs, F. W.; Robertson, C. W.;

Zagursky, R. J.; Cocuzza, A. J.; Jensen, M. A.; Baumeister, K. A system for

rapid DNA sequencing with fluorescent chain-terminating

dideoxynucleotides. Science, 1987, 238, 336-341.

[22] Cocuzza, A. J. Total synthesis of 7-iodo-2',3'-dideoxy-7-deazapurine

nucleosides, key intermediates in the preparation of reagents for the

automated sequencing of DNA. Tetrahedron Lett., 1988, 29(33), 4061-4064.

[23] Seela, F.; Menkhoff, S.; Behrendt, S. Furanoside-pyranoside isomerization of

tubercidin and its 2'-deoxy derivatives: influence of nucleobase and sugar

structure on the proton-catalysed reaction. J. Chem. Soc., Perkin Trans. 2,

1986, 525-530.

[24] Zhang, B.; Bailey, V. C.; Potter, B. V. L. Chemoenzymatic synthesis of 7-

deaza cyclic adenosine 5‘-diphosphate ribose analogues, membrane-

permeant modulators of intracellular calcium release. J. Org. Chem., 2008,

73(5), 1693-1703.

[25] Schneider, K.; Chait, B. T. Increased stability of nucleic acids containing 7-

deaza-guanosine and 7-deaza-adenosine may enable rapid DNA sequencing

by matrix-assisted laser desorption mass spectrometry. Nucleic Acids Res.,

1995, 23(9), 1570-1575.

[26] Li, H.; Peng, X.; Seela, F. Fluorescence quenching of parallel-stranded DNA

bound ethidium bromide: the effect of 7-deaza-2'-deoxyisoguanosine and 7-

halogenated derivatives. Biorg. Med. Chem. Lett., 2004, 14(24), 6031-6034.

[27] Latimer, L. J. P.; Lee, J. S. Ethidium bromide does not fluoresce when

intercalated adjacent to 7-deazaguanine in duplex DNA. J. Biol. Chem.,

1991, 266(21), 13849-13851.

[28] Revankar, G. R.; Robins, R. K. In: Chemistry of Nucleosides and

Nucleotides; Townsend, L. B., Ed. Plenum Press: New York, 1991.

[29] Amarnath, V.; Madhav, R. A survey of methods for the preparation of

pyrrolopyrimidines. Synthesis, 1974, 837-859.

[30] Seela, F.; Peng, X. Synthesis and Properties of 7-Substituted 7-Deazapurine

(Pyrrolo[2,3-d]pyrimidine) 2’-Deoxyribonucleosides. In: Current Protocols

in Nucleic Acid Chemistry; Harkins, E. W., Ed.; John Wiley & Sons: 2005;

Vol. 1, pp. 1.10.1-1.10.20.

[31] Seela, F.; Peng, X. Progress in 7-deazapurine - pyrrolo[2,3-d]pyrimidine -

ribonucleoside synthesis. Curr. Top. Med. Chem., 2006, 6, 867-892.

[32] Isono, K. Current progress on nucleoside antibiotics. Pharmacol. Ther.,

1991, 52(3), 269-286.

[33] Winkeler, H.-D.; Seela, F. Synthesis of 2-amino-7-(2'-deoxy- -D-erythro-

pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one, a new iso-

stere of 2'-deoxyguanosine. J. Org. Chem., 1983, 48(18), 3119-3122.

[34] Seela, F.; Westermann, B.; Bindig, U. Liquid-liquid and solid-liquid phase-

transfer glycosylation of pyrrolo[2,3-d]pyrimidines: stereospecific synthesis

of 2-deoxy- -D-ribofuranosides related to 2'-deoxy-7-carbaguanosine. J.

Chem. Soc., Perkin Trans. 1, 1988, 697-702.

[35] Kondo, T.; Ohgi, T.; Goto, T. Synthesis of 5-methyltubercidin and its -

anomer via condensation of the anion of 4-methoxy-5-methyl-2-

methylthiopyrrolo[2,3-d]pyrimidine and 2,3,5-Tri-O-benzyl-D-ribofuranosyl

Bromide. Agric. Biol. Chem., 1977, 41(8), 1501-1507.

[36] Ohgi, T.; Kondo, T.; Goto, T. Total synthesis of nucleoside Q. Tetrahedron

Lett., 1977, 18(46), 4051-4054.

[37] Lüpke, U.; Seela, F. 7-( -D-Arabinofuranosyl)pyrrolo[2,3-d]pyrimidin-

4(3H)-on – das 7-desazaderivat des antiviralen Nucleosids Ara-H. Chem.

Ber., 1979, 112(10), 3432-3440.

[38] Kazimierczuk, Z.; Cottam, H. B.; Revankar, G. R.; Robins, R. K. Synthesis

of 2'-deoxytubercidin, 2'-deoxyadenosine, and related 2'-deoxynucleosides

via a novel direct stereospecific sodium salt glycosylation procedure. J. Am.

Chem. Soc., 1984, 106(21), 6379-6382.

[39] Cottam, H. B.; Kazimierczuk, Z.; Geary, S.; McKernan, P. A.; Revankar, G.

R.; Robins, R. K. Synthesis and biological activity of certain 6-substituted

and 2,6-disubstituted 2'-deoxytubercidins prepared via the stereospecific

sodium salt glycosylation procedure. J. Med. Chem., 1985, 28(10), 1461-

1467.

[40] Suhadolnik, R. J.; Finkel, S. I.; Chassy, B. M. Nucleoside antibiotics. J. Biol.

Chem., 1968, 243(12), 3532-3537.

[41] Hoffer, M. -Thymidin. Chem. Ber., 1960, 93(12), 2777-2781.

[42] mejkal, J.; orm, F. Nucleic acids components and their analogues. LIII.

Preparation of 1-2'-deoxy- -L-ribofuranosylthymine, "L-thymine". Collect.

Czech. Chem. Commun., 1964, 29, 2809-2813.

[43] Seela, F.; Hasselmann, D.; Winkeler, H.-D. Synthese von -7-

Desazaguanosin und Einfluß der Basenkonzentration auf die

Phasentransferglycosylierung. Liebigs Ann. Chem., 1982, 499-506.

[44] Seela, F.; Winkeler, H.-D. Synthese des -Anomeren von ara-7-

Desazaguanosin durch Phasentransferglycosylierung – Steuerung des

Anomerenverhältnisses durch das quartäre Ammoniumsalz. Liebigs Ann.

Chem., 1982, 1634-1642.

[45] Seela, F.; Kehne, A.; Winkeler, H.-D. Synthese von Acyclo-7-

desazaguanosin durch regiospezifische Phasentransferalkylierung von 2-

Amino-4-methoxy-7H-pyrrolo-[2,3-d]pyrimidin. Liebigs Ann. Chem., 1983,

137-146.

[46] Hansson, C.; Wickberg, B. Selective dealkylation of activated aromatic

ethers. Synthesis, 1976, 191-192.

[47] Winkeler, H.-D.; Seela, F. Synthese und Furanosid/Pyranosid-Isomerisierung

von 7-Desaza-2'-desoxy-7-methylguanosin. Liebigs Ann. Chem., 1984, 708-

721.

[48] Seela, F.; Kehne, A. 2'-Desoxytubercidin – Synthese eines 2'-

Desoxyadenosin-Isosteren durch Phasentransferglycosylierung. Liebigs Ann.

Chem., 1983, 876-884.

[49] Seela, F.; Menkhoff, S. Synthese von 7-Desaza-2'-desoxyinosin durch

Phasentransferglycosylierung. Liebigs Ann. Chem., 1985, 1360-1366.

[50] Davoll, J. Pyrrolo[2,3-d]pyrimidines. J. Chem. Soc., 1960, 131-138.

[51] Seela, F.; Steker, H. Synthese von 2'-Desoxyribofuranosiden des 7H-Pyrrolo

[2,3-d]pyrimidins: Einfluß des C-2-Substituenten auf die Fluoreszenz.

Liebigs Ann. Chem., 1984, 1719-1730.

[52] Seela, F.; Steker, H. ara-7-Desazanebularin – Synthese eines fluoreszieren-

den Pyrrolo[2,3-d]pyrimidin-Nucleosids durch Phasentransferglycosylierung.

Liebigs Ann. Chem., 1983, 1576-1587.

[53] Seela, F.; Steker, H.; Driller, H.; Bindig, U. 2-Amino-2'-desoxytubercidin

und verwandte Pyrrolo[2,3-d]pyrimidinyl-2'-desoxyribofuranoside. Liebigs

Ann. Chem., 1987, 15-19.

[54] Winkeler, H.-D.; Seela, F. 4-Amino-7-( -D-arabinofuranosyl)pyrrolo[2,3-

d]pyrimidin –die Synthese von Ara-Tubercidin durch Phasentransferkatalyse.

Chem. Ber., 1980, 113(6), 2069-2080.

[55] Seela, F.; Becher, G. Synthesis, base pairing, and fluorescence properties of

oligonucleotides containing 1H-Pyrazolo[3,4-d]pyrimidin-6-amine (8-aza-7-

deazapurin-2-amine) as an analogue of purin-2-amine. Helv. Chim. Acta,

2000, 83(5), 928-942.

[56] Seela, F.; Ding, P.; Budow, S. DNA gold nanoparticle conjugates

incorporating thiooxonucleosides: 7-deaza-6-thio-2'-deoxyguanosine as gold

surface anchor. Bioconjugate Chem., 2011, in press.

[57] Seela, F.; Menkhoff, S. 4,4'-Dimethoxy-2,2'-bis(methylthio)-7,7'-methylen-

di(7H-pyrrolo[2,3-d]pyrimidin) – Phasentransferkatalysierte Aglyconver-

brückung in Dichlormethan. Liebigs Ann. Chem., 1982, 1405-1408.

[58] Seela, F.; Driller, H. 7-( -D-Arabinofuranosyl)-2,4-dichlor-7H-pyrrolo[2,3-

d]pyrimidin- Synthese, selektiver Halogenaustausch und Einfluß

glyconischer Schutzgruppen auf die Reaktivität des Aglycons. Liebigs Ann.

Chem., 1984, 722-733.

[59] Soula, G. Tris(polyoxaalkyl)amines (trident), a new class of solid-liquid

phase-transfer catalysts. J. Org. Chem., 1985, 50(20), 3717-3721.

[60] Lüpke, U.; Seela, F. Ribosidierung von 7H-Pyrrolo[2,3-d]pyrimidin-4(3H)-

on an N-3. Chem. Ber., 1979, 112(10), 3526-3529.

[61] Seela, F.; Muth, H.-P.; Bindig, U. Synthesis of 6-substituted 7-carbapurine

2',3'-dideoxynucleosides: solid-liquid phase-transfer glycosylation of 4-

chloropyrrolo[2,3-d]pyrimidine and deoxygenation of its 2'-

deoxyribofuranoside. Synthesis, 1988, 670-674.

[62] Seela, F.; Driller, H. 7-Deaza-2 -deoxy-O6-methylguanosine: selective N

2-

formylation via a formamidine, phosphoramidite synthesis and properties of

oligonucleotides. Nucleosides Nucleotides, 1989, 8(1), 1-21.

[63] Ramzaeva, N.; Seela, F. 7-Substituted 7-deaza-2 -deoxyguanosines:

regioselective halogenation of pyrrolo[2,3-d]pyrimidine nucleosides. Helv.

Chim. Acta, 1995, 78(5), 1083-1090.

[64] Seela, F.; Shaikh, K. 7-Halogenated 7-deaza-2 -deoxyxanthine 2 -

deoxyribonucleosides. Helv. Chim. Acta, 2004, 87(6), 1325-1332.

[65] Ramzaeva, N.; Becher, G.; Seela, F. Facile synthesis of 2'-deoxynucleoside

analogs of preQ. Synthesis, 1998, 1327-1330.

[66] Ming, X.; Seela, F. Efficient synthesis of the tRNA nucleoside preQ0, 7-

cyano-7-deazaguanosine, via microwave-assisted iodo carbonitrile

exchange. Chem. Biodivers., 2010, 7, 2616-2621.

[67] Seela, F.; Xu, K.; Chittepu, P. Fluorinated pyrrolo[2,3-d]pyrimidine

nucleosides: 7-fluoro-7-deazapurine 2'-deoxyribofuranosides and 2'-deoxy-

2'-fluoroarabinofuranosyl derivatives. Synthesis, 2006, 2005-2012.


[68] Seela, F.; Chittepu, P.; He, Y.; He, J.; Xu, K. 6-Azapyrimidine and 7-

deazapurine 2 -deoxy-2 -fluoroarabinonucleosides: synthesis, conformation

and properties of oligonucleotides. Nucleosides Nucleotides Nucleic Acids,

2005, 24(5), 847-850.

[69] Seela, F.; Xu, K.; Chittepu, P.; Ming, X. Fluorinated 7-deazapurine 2 -

deoxyribonucleosides: modification at the nucleobase and the sugar moiety.

Nucleosides Nucleotides Nucleic Acids, 2007, 26(6), 607-610.

[70] Seela, F.; Peng, X. Regioselective syntheses of 7-halogenated 7-deazapurine

nucleosides related to 2-amino-7-deaza-2'-deoxyadenosine and 7-deaza-2'-

deoxyisoguanosine. Synthesis, 2004, 1203-1210.

[71] Seela, F.; Chen, Y. Methylated DNA: the influence of 7-deaza-7-

methylguanine on the structure and stability of oligonucleotides. Helv. Chim.

Acta, 1997, 80(4), 1073-1086.

[72] Pudlo, J. S.; Nassiri, M. R.; Kern, E. R.; Wotring, L. L.; Drach, J. C.;

Townsend, L. B. Synthesis, antiproliferative, and antiviral activity of certain

4-substituted and 4,5-disubstituted 7-[(1,3-dihydroxy-2-

propoxy)methyl]pyrrolo[2,3-d]pyrimidines. J. Med. Chem., 1990, 33(7),

1984-1992.

[73] Wang, X.; Seth, P. P.; Ranken, R.; Swayze, E. E.; Migawa, M. T. Synthesis

and biological activity of 5-fluorotubercidin. Nucleosides Nucleotides

Nucleic Acids, 2004, 23(1), 161-170.

[74] Seela, F.; Thomas, H. Synthesis of certain 5-substituted 2 -deoxytubercidin

derivatives. Helv. Chim. Acta, 1994, 77(4), 897-903.

[75] Seela, F.; Zulauf, M. Palladium-catalyzed cross coupling of 7-iodo-2'-

deoxytubercidin with terminal alkynes. Synthesis, 1996, 726-730.

[76] Ramzaeva, N.; Mittelbach, C.; Seela, F. 7-Halogenated 7-deaza-2 -

deoxyinosines. Helv. Chim. Acta, 1999, 82(1), 12-18.

[77] Seela, F.; Rosemeyer, H.; Zulauf, M.; Chen, Y.; Kastner, G.; Reuter, H. 7-

Nitro-7-deaza-2'-deoxyadenosine and 8-methyl-7-deaza-2'-deoxyguanosine:

pyrrolo[2,3-d]pyrimidine nucleosides with different sugar conformations.

Liebigs Ann./Recueil, 1997, 2525-2530.

[78] Kawate, T.; Allerson, C. R.; Wolfe, J. L. Regioselective syntheses of 7-nitro-

7-deazapurine nucleosides and nucleotides for efficient PCR incorporation.

Org. Lett., 2005, 7(18), 3865-3868.

[79] Kawate, T.; Wang, B. H.; Allerson, C. R.; Wolfe, J. L. Synthesis and

application of nitro-substituted nucleosides and nucleotides. Synthesis, 2006,

3280-3290.

[80] Wolfe, J. L.; Kawate, T.; Sarracino, D. A.; Zillmann, M.; Olson, J.; Stanton,

Jr., V. P.; Verdine, G. L. A genotyping strategy based on incorporation and

cleavage of chemically modified nucleotides. Proc. Natl. Acad. Sci. USA,

2002, 99(17), 11073-11078.

[81] Min, C.; Cushing, T. D.; Verdine, G. L. Template-directed interference

footprinting of protein adenine contacts. J. Am. Chem. Soc., 1996, 118(26),

6116-6120.

[82] Seela, F.; Schweinberger, E.; Xu, K.; Sirivolu, V. R.; Rosemeyer, H.;

Becker, E.-M. 1,N6-Etheno-2'-deoxytubercidin and pyrrolo-C: synthesis,

base pairing, and fluorescence properties of 7-deazapurine nucleosides and

oligonucleotides. Tetrahedron, 2007, 63(17), 3471-3482.

[83] Peng, X.; Li, H.; Seela, F. pH-Dependent mismatch discrimination of

oligonucleotide duplexes containing 2 -deoxytubercidin and 2- or 7-

substituted derivatives: protonated base pairs formed between 7-deazapurines

and cytosine. Nucleic Acids Res., 2006, 34(20), 5987-6000.

[84] Seela, F.; Xu, K. 7-Halogenated 7-deazapurine 2 -deoxyribonucleosides

related to 2 -deoxyadenosine, 2 -deoxyxanthosine, and 2 -deoxyisoguanosine:

syntheses and properties. Helv. Chim. Acta, 2008, 91(6), 1083-1105.

[85] Kazimierczuk, Z.; Mertens, R.; Kawczynski, W.; Seela, F. 2 -

Deoxyisoguanosine and base-modified analogues: chemical and

photochemical synthesis. Helv. Chim. Acta, 1991, 74(8), 1742-1748.

[86] Seela, F.; Wei, C. The base-pairing properties of 7-deaza-2 -

deoxyisoguanosine and 2 -deoxyisoguanosine in oligonucleotide duplexes

with parallel and antiparallel chain orientation. Helv. Chim. Acta, 1999,

82(5), 726-745.

[87] Balow, G.; Mohan, V.; Lesnik, E. A.; Johnston, J. F.; Monia, B. P.; Acevedo,

O. L. Biophysical and antisense properties of oligodeoxynucleotides

containing 7-propynyl-, 7-iodo- and 7-cyano-7-deaza-2-amino-2 -

deoxyadenosines. Nucleic Acids Res., 1998, 26(14), 3350-3357.

[88] Seela, F.; Peng, X.; Li, H.; Chittepu, P.; Shaikh, K. I.; He, J.; He, Y.;

Mikhailopulo, I. Modified DNA: from synthesis to molecular recognition.

Collect. Symp. Series, 2005, 7, 1-20.

[89] Sepiol, J.; Kazimierczuk, Z.; Shugar, D. Tautomerism of isoguanosine and

solvent-induced keto-enol equilibrium. Z. Naturforsch., C: Biosci., 1976,

31(7-8), 361-370.

[90] Robinson, H.; Gao, Y.-G.; Bauer, C.; Roberts, C.; Switzer, C.; Wang, A. H.-

J. 2‘-Deoxyisoguanosine adopts more than one tautomer to form base pairs

with thymidine observed by high-resolution crystal structure analysis.

Biochemistry, 1998, 37(31), 10897-10905.

[91] Switzer, C.; Moroney, S. E.; Benner, S. A. Enzymatic incorporation of a new

base pair into DNA and RNA. J. Am. Chem. Soc., 1989, 111(21), 8322-8323.

[92] Martinot, T. A.; Benner, S. A. Artificial genetic systems: exploiting the

“aromaticity” formalism to improve the tautomeric ratio for isoguanosine

derivatives. J. Org. Chem., 2004, 69(11), 3972-3975.

[93] Seela, F.; Peng, X.; Li, H. Base-pairing, tautomerism, and mismatch

discrimination of 7-halogenated 7-deaza-2‘-deoxyisoguano-

sine: oligonucleotide duplexes with parallel and antiparallel chain

orientation. J. Am. Chem. Soc., 2005, 127(21), 7739-7751.

[94] Seela, F.; Wei, C.; Reuter, H.; Kastner, G. 7-Deaza-2'-deoxyisoguanosine

adopts the form of an N1-H,2-keto tautomer. Acta Crystallogr., Sect. C:

Cryst. Struct. Commun., 1999, 55(8), 1335-1337.

[95] Seela, F.; Chen, Y.; Sauer, M. Synthesis of 2 ,3 -didehydro-2 ,3 -

dideoxyisoinosine and oxidation of fluorescent 2-hydroxypurine nucleosides

by xanthine oxidase. Nucleosides Nucleotides, 1998, 17(1), 39-52.

[96] Seela, F.; Liman, U. ara-7-Desazaxanthosin – ein Xanthin-Nucleosid mit

stabiler N-glycosylischer Bindung. Liebigs Ann. Chem., 1984, 273-282.

[97] Seela, F.; Chen, Y.; Bindig, U.; Kazimierczuk, Z. Synthesis of 2 -

deoxyisoinosine and related 2 -deoxyribonucleosides. Helv. Chim. Acta,

1994, 77(1), 194-202.

[98] Seela, F.; Becher, G.; Chen, Y. Fluorescence properties and base pair

stability of oligonucleotides containing 8-aza-7-deaza-2 -deoxyisoinosine or

2 -deoxyisoinosine. Nucleosides Nucleotides Nucleic Acids, 2000, 19(10),

1581-1598.

[99] Seela, F.; Winkeler, D. Bevorzugte -Glycosidbildung durch Phasentransfer-

Katalyse bei der Synthese von D-Arabinofuranosyl-7-desazapurinnucleosi-

den. Angew. Chem., 1979, 91(7), 570-571.

[100] Buhr, C. A.; Wagner, R. W.; Grant, D.; Froehler, B. C.

Oligodeoxynucleotides containing C-7 propyne analogs of 7-deaza-2 -

deoxyguanosine and 7-deaza-2 -deoxyadenosine. Nucleic Acids Res., 1996,

24(15), 2974-2980.

[101] Ramasamy, K.; Robins, R. K.; Revankar, G. R. Total and stereospecific

synthesis of 2'-deoxycadeguomycin. J. Chem. Soc., Chem. Commun., 1989,

560-562.

[102] Edstrom, E. D.; Wei, Y. A new synthetic route to -2'-deoxyribosyl-5-

substituted pyrrolo[2,3-d]pyrimidines. Synthesis of 2'-deoxycadeguomycin.

J. Org. Chem., 1995, 60(16), 5069-5076.

[103] Ramasamy, K.; Imamura, N.; Robins, R. K.; Revankar, G. R. A Facile and

improved synthesis of tubercidin and certain related pyrrolo[2,3-

d]pyrimidine nucleosides by the stereospecific sodium salt glycosylation

procedure. J. Heterocycl. Chem., 1988, 25, 1893-1898.

[104] Revankar, G. R.; Robins, R. K. Use of the sodium salt glycosylation in

nucleoside synthesis. Nucleosides Nucleotides, 1989, 8(5), 709-724.

[105] Ramasamy, K.; Imamura, N.; Robins, R. K.; Revankar, G. R. A facile

synthesis of tubercidin and related 7-deazapurine nucleosides via the

stereospecific sodium salt glycosylation procedure. Tetrahedron Lett., 1987,

28(43), 5107-5110.

[106] Ramasamy, K.; Robins, R. K.; Revankar, G. R. Total synthesis of 2'-

deoxytoyocamycin, 2'-deoxysangivamycin and related 7- -D-

arabinofuranosylpyrrolo[2,3-d]pyrimidines via ring closure of pyrrole

precursors prepared by the stereospecific sodium salt glycosylation

procedure. Tetrahedron, 1986, 42(21), 5869-5878.

[107] Noell, C. W.; Robins, R. K. Aromaticity in heterocyclic systems. II. The

application of N.M.R. in a study of the synthesis and structure of certain

imidazo[1,2-c]pyrimidines and related pyrrolo[2,3-d]pyrimidines. J.

Heterocycl. Chem., 1964, 1(1), 34-41.

[108] Seela, F.; Driller, H.; Liman, U. 7-Desaza-Isostere von 2'-Desoxyxanthosin

und 2'-Desoxyspongosin – Synthese via Glycosylierung von 2,4-Dichlor-7H-

pyrrolo[2,3-d]pyrimidin. Liebigs Ann. Chem., 1985, 312-320.

[109] Seela, F.; Wiglenda, T.; Rosemeyer, H.; Eickmeier, H.; Reuter, H. 7-Deaza-

2 -deoxyxanthosine dihydrate forms water-filled nanotubes with C H· · ·O

hydrogen bonds. Angew. Chem. Int. Ed., 2002, 41(4), 603-605.

[110] Ramasamy, K.; Joshi, R. V.; Robins, R. K.; Revankar, G. R. Total and

stereospecific synthesis of cadeguomycin, 2'-deoxycadeguomycin, ara-

cadeguomycin, and certain related nucleosides. J. Chem. Soc., Perkin Trans.

1, 1989, 2375-2384.

[111] Goodman, L. In: Basic Principles in Nucleic Acid Chemistry; Ts'o, P. O. P.,

Ed.; Academic Press: New York, 1974; Vol. 1.

[112] Moffatt, J. G. In: Nucleoside Analogues: Chemistry, Biology, and Medical

Applications; Walker, R. T.; De Clercq, E.; Eckstein, F., Eds.; Plenum Press:

New York, 1979.

[113] Vorbrüggen, H.; Ruh-Pohlenz, C. Handbook of Nucleoside Synthesis; Wiley-

Interscience: New York, 2001.

[114] Robins, M. J.; Muhs, W. H. Synthesis of 2'-deoxytubercidin {4-amino-7-(2-

deoxy- -D-erythro-pentofuranosyl)pyrrolo[2,3-d]pyrimidine} from the

parent antibiotic. J. Chem. Soc., Chem. Commun., 1976, 269-269.

[115] Barton, D. H. R.; McCombie, S. W. A new method for the deoxygenation of

secondary alcohols. J. Chem. Soc., Perkin Trans. 1, 1975, 1574-1585.

[116] Robins, M. J.; Wilson, J. S. Smooth and efficient deoxygenation of

secondary alcohols. A general procedure for the conversion of

ribonucleosides to 2'-deoxynucleosides. J. Am. Chem. Soc., 1981, 103(4),

932-933.

[117] Robins, M. J.; Wilson, J. S.; Hansske, F. Nucleic acid related compounds. 42.

A general procedure for the efficient deoxygenation of secondary alcohols.

Regiospecific and stereoselective conversion of ribonucleosides to 2'-

deoxynucleosides. J. Am. Chem. Soc., 1983, 105(12), 4059-4065.

[118] Markiewicz, W. T.; Payukova, N. S.; Samek, Z.; Smrt, J. J. The reaction of

1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane with cytosine arabinoside and

1-(6-deoxy- -L-talofuransyl)uracil. Collect. Czech. Chem. Commun., 1980,

45, 1860-1865.


[119] Jain, T. C.; Russell, A. F.; Moffatt, J. G. Reactions of 2-acyloxyisobutyryl

halides with nucleosides. III. Reactions of tubercidin and formycin. J. Org.

Chem., 1973, 38(18), 3179-3186.

[120] Robins, M. J.; Jones, R. A.; Mengel, R. Nucleic acid related compounds. 24.

Transformation of tubercidin 2',3'-O-orthoacetate into halo, deoxy, epoxide,

and unsaturated sugar nucleosides. Can. J. Chem., 1977, 55(7), 1251-1259.

[121] Krawczyk, S. H.; Townsend, L. B. 2 ,3 -Dideoxyadenosine analogs of the

nucleoside antibiotics tubercidin, toyocamycin and sangivamycin.

Nucleosides Nucleotides, 1989, 8(1), 97-115.

[122] Seela, F.; Rosemeyer, H.; Gumbiowski, R.; Mersmann, K.; Muth, H.-P.;

Röling, A. Base-modified purine 2 ,3 -dideoxyribonucleosides: synthesis via

deoxygenation or direct nucleobase anion glycosylation. Nucleosides

Nucleotides, 1991, 10(1), 409-412.

[123] Saito, Y.; Kato, K.; Umezawa, K. Synthesis and structure-activity

relationship of ribofuranosyl echiguanine analogs as inhibitors of

phosphatidylinositol 4-kinase. Tetrahedron, 1998, 54(17), 4251-4266.

[124] Seela, F.; Zulauf, M. 7-Deazaadenine-DNA: bulky 7-iodo substituents or

hydrophobic 7-hexynyl chains are well accommodated in the major groove

of oligonucleotide duplexes. Chem. Eur. J., 1998, 4(9), 1781-1790.

[125] Okamoto, A.; Taiji, T.; Tanaka, K.; Saito, I. Synthesis and duplex stability of

oligonucleotides containing 7-vinyl-7-deazaguanine as a strong electron-

donating nucleobase. Tetrahedron Lett., 2000, 41(51), 10035-10039.

[126] Booth, J.; Cummins, W. J.; Brown, T. An analogue of adenine that forms an

"A:T" base pair of comparable stability to G:C. Chem. Commun., 2004,

2208-2209.

[127] Rosemeyer, H.; Ramzaeva, N.; Becker, E.-M.; Feiling, E.; Seela, F.

Oligonucleotides incorporating 7-(aminoalkynyl)-7-deaza-2‘-

deoxyguanosines: duplex stability and phosphodiester hydrolysis by

exonucleases. Bioconjugate Chem., 2002, 13(6), 1274-1285.

[128] Bowers, J.; Mitchell, J.; Beer, E.; Buzby, P. R.; Causey, M.; Efcavitch, J. W.;

Jarosz, M.; Krzymanska-Olejnik, E.; Kung, L.; Lipson, D.; Lowman, G. M.;

Marappan, S.; McInerney, P.; Platt, A.; Roy, A.; Siddiqi, S. M.; Steinmann,

K.; Thompson, J. F. Virtual terminator nucleotides for next-generation DNA

sequencing. Nat. Methods, 2009, 6(8), 593-595.

[129] Turcatti, G.; Romieu, A.; Fedurco, M.; Tairi, A.-P. A new class of cleavable

fluorescent nucleotides: synthesis and optimization as reversible terminators

for DNA sequencing by synthesis. Nucleic Acids Res., 2008, 36(4), e25.

[130] Ju, J.; Kim, D. H.; Bi, L.; Meng, Q.; Bai, X.; Li, Z.; Li, X.; Marma, M. S.;

Shi, S.; Wu, J.; Edwards, J. R.; Romu, A.; Turro, N. J. Four-color DNA

sequencing by synthesis using cleavable fluorescent nucleotide reversible

terminators. Proc. Natl. Acad. Sci. USA, 2006, 103(52), 19635-19640.

[131] Guo, J.; Yu, L.; Turro, N. J.; Ju, J. An integrated system for DNA sequencing

by synthesis using novel nucleotide analogues. Acc. Chem. Res., 2010, 43(4),

551-563.

[132] Bi, L.; Kim, D. H.; Ju, J. Design and synthesis of a chemically cleavable

fluorescent nucleotide, 3‘-O-Allyl-dGTP-allyl-Bodipy-FL-510, as a

reversible terminator for DNA sequencing by synthesis. J. Am. Chem. Soc.,

2006, 128(8), 2542-2543.

[133] Meng, Q.; Kim, D. H.; Bai, X.; Bi, L.; Turro, N. J.; Ju, J. Design and

synthesis of a photocleavable fluorescent nucleotide 3‘-O-allyl-dGTP-PC-

Bodipy-FL-510 as a reversible terminator for DNA sequencing by synthesis.

J. Org. Chem., 2006, 71(8), 3248-3252.

[134] Jäger, S.; Rasched, G.; Kornreich-Leshem, H.; Engeser, M.; Thum, O.;

Famulok, M. A versatile toolbox for variable DNA functionalization at high

density. J. Am. Chem. Soc., 2005, 127(43), 15071-15082.

[135] Huisgen, R. Kinetics and reaction mechanisms: selected examples from the

experience of forty years. Pure Appl. Chem., 1989, 61(4), 613-628.

[136] Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, K. B. A stepwise

Huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation”

of azides and terminal alkynes. Angew. Chem. Int. Ed., 2002, 41(14), 2596-

2599.

[137] Amblard, F.; Cho, J. H.; Schinazi, R. F. Cu(I)-catalyzed Huisgen

azide alkyne 1,3-dipolar cycloaddition reaction in nucleoside, nucleotide,

and oligonucleotide chemistry. Chem. Rev., 2009, 109(9), 4207-4220.

[138] Ramzaeva, N.; Mittelbach, C.; Seela, F. 7-Deazaguanine DNA:

Oligonucleotides with hydrophobic or cationic side chains. Helv. Chim. Acta,

1997, 80(6), 1809-1822.

[139] Seela, F.; Sirivolu, V. R.; Chittepu, P. Modification of DNA with octadiynyl

side chains: synthesis, base pairing, and formation of fluorescent coumarin

dye conjugates of four nucleobases by the alkyne azide “click” reaction.

Bioconjugate Chem., 2008, 19(1), 211-224.

[140] Seela, F.; Ingale, S. A. “Double click” reaction on 7-deazaguanine DNA:

synthesis and excimer fluorescence of nucleosides and oligonucleotides with

branched side chains decorated with proximal pyrenes. J. Org. Chem., 2010,

75(2), 284-295.

[141] Leonard, P.; Ingale, S. A.; Seela, F. Unpublished results. 2010.

[142] Seela, F.; Zulauf, M. Oligonucleotides containing 7-deazaadenines: the

influence of the 7-substituent chain length and charge on the duplex stability.

Helv. Chim. Acta, 1999, 82(11), 1878-1898.

[143] Seela, F.; Zulauf, M.; Sauer, M.; Deimel, M. 7-Substituted 7-deaza-2 -

deoxyadenosines and 8-aza-7-deaza-2 -deoxyadenosines: fluorescence of

DNA-base analogues induced by the 7-alkynyl side chain. Helv. Chim. Acta,

2000, 83(5), 910-927.

[144] Seela, F.; Ramzaeva, N.; Leonard, P.; Chen, Y.; Debelak, H.; Feiling, E.;

Kröschel, R.; Zulauf, M.; Wenzel, T.; Fröhlich, T.; Kostrzewa, M.

Phosphoramidites and oligonucleotides containing 7-deazapurines and

pyrimidines carring aminopropargyl side chains. Nucleosides Nucleotides

Nucleic Acids, 2001, 20(4), 1421-1424.

[145] Ming, X.; Leonard, P.; Heindl, D.; Seela, F. Azide-alkyne "click" reaction

performed on oligonucleotides with the universal nucleoside 7-octadiynyl-7-

deaza-2'-deoxyinosine. Nucleic Acids Symp. Ser., 2008, 52, 471-472.

[146] Seela, F.; Ming, X. Oligonucleotides containing 7-deaza-2 -deoxyinosine as

universal nucleoside: synthesis of 7-halogenated and 7-alkynylated

derivatives, ambiguous base pairing, and dye functionalization by the

alkyne–azide ‘click’ reaction. Helv. Chim. Acta, 2008, 91(7), 1181-1200.

[147] Seela, F.; Shaikh, K. I. Oligonucleotides containing 7-propynyl-7-

deazaguanine: synthesis and base pair stability. Tetrahedron, 2005, 61(10),

2675-2681.

[148] Seela, F.; Budow, S.; Shaikh, K. I.; Jawalekar, A. M. Stabilization of tandem

dG-dA base pairs in DNA-hairpins: replacement of the canonical bases by 7-

deaza-7-propynylpurines. Org. Biomol. Chem., 2005, 3(23), 4221-4226.

[149] Seela, F.; Ding, P. Unpublished results. 2010.

[150] Brázdilová, P.; Vrábel, M.; Pohl, R.; Pivo ková, H.; Havran, L.; Hocek, M.;

Fojta, M. Ferrocenylethynyl derivatives of nucleoside triphosphates:

synthesis, incorporation, electrochemistry, and bioanalytical applications.

Chem. Eur. J., 2007, 13(34), 9527-9533.

[151] Vrábel, M.; Horáková, P.; Pivo ková, H.; Kalachova, L.; ernocká, H.;

Cahová, H.; Pohl, R.; ebest, P.; Havran, L.; Hocek, M.; Fojta, M. Base-

modified DNA Labeled by [Ru(bpy)3]2+

and [Os(bpy)3]2+

complexes:

Construction by polymerase incorporation of modified nucleoside

triphosphates, electrochemical and luminescent properties, and applications.

Chem. Eur. J., 2009, 15(5), 1144-1154.

[152] Ikonen, S.; Mací ková-Cahová, H.; Pohl, R.; anda, M.; Hocek, M.

Synthesis of nucleoside and nucleotide conjugates of bile acids, and

polymerase construction of bile acid-functionalized DNA. Org. Biomol.

Chem., 2010, 8(5), 1194-1201.

[153] apek, P.; Cahová, H.; Pohl, R.; Hocek, M.; Gloeckner, C.; Marx, A. An

efficient method for the construction of functionalized DNA bearing amino

acid groups through cross-coupling reactions of nucleoside triphosphates

followed by primer extension or PCR. Chem. Eur. J., 2007, 13(21), 6196-

6203.

[154] Vrábel, M.; Pohl, R.; Votruba, I.; Sajadi, M.; Kovalenko, S. A.; Ernsting, N.

P.; Hocek, M. Synthesis and photophysical properties of 7-deaza-2'-

deoxyadenosines bearing bipyridine ligands and their Ru(II)-complexes in

position 7. Org. Biomol. Chem., 2008, 6(16), 2852-2860.

[155] Cahová, H.; Havran, L.; Brázdilová, P.; Pivo ková, H.; Pohl, R.; Fojta, M.;

Hocek, M. Aminophenyl- and nitrophenyl-labeled nucleoside triphosphates:

synthesis, enzymatic incorporation, and electrochemical detection. Angew.

Chem. Int. Ed., 2008, 47(11), 2059-2062.

[156] Raindlová, V.; Pohl, R.; anda, M.; Hocek, M. Direct polymerase synthesis

of reactive aldehyde-functionalized DNA and its conjugation and staining

with hydrazines. Angew. Chem. Int. Ed., 2010, 49(6), 1064-1066.

[157] Seela, F.; Shaikh, K.; Eickmeier, H. 7-Deaza-2 -deoxy-7-propynylguanosine.

Acta Crystallogr., Sect. C: Cryst. Struct. Commun., 2004, 60(7), o489-o491.

[158] Seela, F.; Shaikh, K. I.; Budow, S.; Eickmeier, H. 2 -Deoxy-7-propynyl-7-

deazaadenosine: a DNA duplex-stabilizing nucleoside. Acta Crystallogr.,

Sect. C: Cryst. Struct. Commun., 2006, 62(5), o246-o248.

[159] Meldal, M.; Tornøe, C. W. Cu-catalyzed azide alkyne cycloaddition. Chem.

Rev., 2008, 108(8), 2952-3015.

[160] Kolb, H. C.; Finn, M. G.; Sharpless, K. B. Click chemistry: diverse chemical

function from a few good reactions. Angew. Chem. Int. Ed., 2001, 40(11),

2004-2021.

[161] Moses, J. E.; Moorhouse, A. D. The growing applications of click chemistry.

Chem. Soc. Rev., 2007, 36(8), 1249-1262.

[162] Seela, F.; Sirivolu, V. R. Nucleosides and oligonucleotides with diynyl side

chains: base pairing and functionalization of 2 -deoxyuridine derivatives by

the copper(I)-catalyzed alkyne azide ‘click’ cycloaddition. Helv. Chim. Acta,

2007, 90(3), 535-552.

[163] Seela, F.; Sirivolu, V. R. DNA containing side chains with terminal triple

bonds: base pair stability and functionalization of alkynylated pyrimidines

and 7-deazapurines. Chem. Biodivers., 2006, 3, 509-514.

[164] Kolb, H. C.; Sharpless, K. B. The growing impact of click chemistry on drug

discovery. Drug Discov. Today, 2003, 8(24), 1128-1137.

[165] Gramlich, P. M. E.; Wirges, C. T.; Manetto, A.; Carell, T. Postsynthetic

DNA modification through the copper-catalyzed azide–alkyne cycloaddition

reaction. Angew. Chem. Int. Ed., 2008, 47(44), 8350-8358.

[166] Gogoi, K.; Mane, M. V.; Kunte, S. S.; Kumar, V. A. A versatile method for

the preparation of conjugates of peptides with DNA/PNA/analog by

employing chemo-selective click reaction in water. Nucleic Acids Res., 2007,

35(21), e139.

[167] Chittepu, P.; Sirivolu, V. R.; Seela, F. Nucleosides and oligonucleotides

containing 1,2,3-triazole residues with nucleobase tethers: synthesis via the

azide-alkyne 'click' reaction. Biorg. Med. Chem., 2008, 16(18), 8427-8439.

[168] Jawalekar, A. M.; Meeuwenoord, N.; Cremers, J. G. O.; Overkleeft, H. S.;

van der Marel, G. A.; Rutjes, F. P. J. T.; van Delft, F. L. Conjugation of

nucleosides and oligonucleotides by [3+2] cycloaddition. J. Org. Chem.,

2008, 73(1), 287-290.


[169] Pourceau, G.; Meyer, A.; Vasseur, J.-J.; Morvan, F. Synthesis of mannose

and galactose oligonucleotide conjugates by bi-click chemistry. J. Org.

Chem., 2009, 74(3), 1218-1222.

[170] Bouillon, C.; Meyer, A.; Vidal, S.; Jochum, A.; Chevolot, Y.; Cloarec, J.-P.;

Praly, J.-P.; Vasseur, J.-J.; Morvan, F. Microwave assisted “click” chemistry

for the synthesis of multiple labeled-carbohydrate oligonucleotides on solid

support. J. Org. Chem., 2006, 71(12), 4700-4702.

[171] Lönnberg, H. Solid-phase synthesis of oligonucleotide conjugates useful for

delivery and targeting of potential nucleic acid therapeutics. Bioconjugate

Chem., 2009, 20(6), 1065-1094.

[172] Devaraj, N. K.; Miller, G. P.; Ebina, W.; Kakaradov, B.; Collman, J. P.;

Kool, E. T.; Chidsey, C. E. D. Chemoselective covalent coupling of

oligonucleotide probes to self-assembled monolayers. J. Am. Chem. Soc.,

2005, 127(24), 8600-8601.

[173] Seo, T. S.; Bai, X.; Ruparel, H.; Li, Z.; Turro, N. J.; Ju, J. Photocleavable

fluorescent nucleotides for DNA sequencing on a chip constructed by site-

specific coupling chemistry. Proc. Natl. Acad. Sci. USA, 2004, 101(15),

5488-5493.

[174] Chevolot, Y.; Bouillon, C.; Vidal, S.; Morvan, F.; Meyer, A.; Cloarec, J.-P.;

Jochum, A.; Praly, J.-P.; Vasseur, J.-J.; Souteyrand, E. DNA-based

carbohydrate biochips: a platform for surface glyco-engineering. Angew.

Chem. Int. Ed., 2007, 46(14), 2398-2402.

[175] Collman, J. P.; Devaraj, N. K.; Chidsey, C. E. D. “Clicking” functionality

onto electrode surfaces. Langmuir, 2004, 20(4), 1051-1053.

[176] Qing, G.; Xiong, H.; Seela, F.; Sun, T. Spatially controlled DNA

nanopatterns by “click” chemistry using oligonucleotides with different

anchoring sites. J. Am. Chem. Soc., 2010, 132(43), 15228-15232.

[177] Gramlich, P. M. E.; Wirges, C. T.; Gierlich, J.; Carell, T. Synthesis of

modified DNA by PCR with alkyne-bearing purines followed by a click

reaction. Org. Lett., 2007, 10(2), 249-251.

[178] Seela, F.; Ingale, S. A. Unpublished results. 2010.

[179] Seela, F.; Ding, P. Manuscript in preparation. 2010.

[180] Seela, F.; Sirivolu, V. R.; Ding, P. Unpublished results. 2010.

[181] Seela, F.; Pujari, S. S. Azide alkyne “click” conjugation of 8-aza-7-

deazaadenine-DNA: synthesis, duplex stability, and fluorogenic dye labeling.

Bioconjugate Chem., 2010, 21(9), 1629-1641.

[182] Seela, F.; Xiong, H.; Leonard, P.; Budow, S. 8-Aza-7-deazaguanine

nucleosides and oligonucleotides with octadiynyl side chains: synthesis,

functionalization by the azide-alkyne 'click' reaction and nucleobase specific

fluorescence quenching of coumarin dye conjugates. Org. Biomol. Chem.,

2009, 7(7), 1374-1387.

[183] Bushmakina, N. G.; Misharin, A. Y. A simple synthesis of 4-amino-2,2,6,6-

tetramethyl-1-piperidinyloxy radical. Synthesis, 1986, 966.

[184] Ding, P.; Wunnicke, D.; Steinhoff, H.-J.; Seela, F. Site-directed spin-labeling

of DNA by the azide–alkyne ‘click’ reaction: nanometer distance

measurements on 7-deaza-2 -deoxyadenosine and 2 -deoxyuridine nitroxide

conjugates spatially separated or linked to a ‘dA-dT’ base pair. Chem. Eur.

J., 2010, 16(48), 14385-14396.

[185] El-Sagheer, A. H.; Brown, T. Click chemistry with DNA. Chem. Soc. Rev.,

2010, 39(4), 1388-1405.

[186] Kumar, R.; El-Sagheer, A.; Tumpane, J.; Lincoln, P.; Wilhelmsson, L. M.;

Brown, T. Template-directed oligonucleotide strand ligation, covalent

intramolecular DNA circularization and catenation using click chemistry. J.

Am. Chem. Soc., 2007, 129(21), 6859-6864.

[187] Lietard, J.; Meyer, A.; Vasseur, J.-J.; Morvan, F. New strategies for

cyclization and bicyclization of oligonucleotides by click chemistry assisted

by microwaves. J. Org. Chem., 2008, 73(1), 191-200.

[188] Peng, X.; Li, H.; Seidman, M. A template-mediated click–click reaction:

PNA–DNA, PNA–PNA (or peptide) ligation, and single nucleotide

discrimination. Eur. J. Org. Chem., 2010, 4194-4197.

[189] Angelov, T.; Guainazzi, A.; Schärer, O. D. Generation of DNA interstrand

cross-links by post-synthetic reductive amination. Org. Lett., 2009, 11(3),

661-664.

[190] Pujari, S. S.; Xiong, H.; Seela, F. Cross-linked DNA generated by “bis-click”

reactions with bis-functional azides: site independent ligation of

oligonucleotides via nucleobase alkynyl chains. J. Org. Chem., 2010, 75(24),

8693-8696.

[191] Limbach, P. A.; Crain, P. F.; McCloskey, J. A. Summary: the modified

nucleosides of RNA. Nucleic Acids Res., 1994, 22(12), 2183-2196.

[192] Seela, F.; Chen, Y.; Zulauf, M. Regioselectivity of the Mannich reaction on

pyrrolo[2,3-d] pyrimidine nucleosides related to 7-deaza-2'-deoxyadenosine

or 7-deaza-2'-deoxyguanosine. Synthesis, 1997, 1067-1072.

[193] Seela, F.; Driller, H. Solid-phase synthesis of the self-complementary

hexamer d(c7GpCpc

7GpCpc

7GpC) via the O-3 -phosphoramidite of 7-deaza-

2 -deoxyguanosine. Nucleic Acids Res., 1985, 13(3), 911-926.

[194] Marquez, V. E.; Tseng, C. K.-H.; Mitsuya, H.; Aoki, S.; Kelley, J. A.; Ford,

Jr., H.; Roth, J. S.; Broder, S.; Johns, D. G.; Driscoll, J. S. Acid-stable 2'-

fluoro purine dideoxynucleosides as active agents against HIV. J. Med.

Chem., 1990, 33(3), 978-985.

[195] Masood, R.; Ahluwalia, G. S.; Cooney, D. A.; Fridland, A.; Marquez, V. E.;

Driscoll, J. S.; Hao, Z.; Mitsuya, H.; Perno, C.-F.; Broder, S.; Johns, D. G. 2'-

Fluoro-2',3'-dideoxyarabinosyladenine: a metabolically stable analogue of

the antiretroviral agent 2',3'-dideoxyadenosine. Mol. Pharmacol., 1990,

37(4), 590-596.

[196] Filler, R.; Naqvi, S. M. In: Organofluorine Chemicals and Their Industrial

Applications; Banks, R. E.; Horwood, E., Eds.; Holsted Press: New York,

1979.

[197] Bergstrom, D. E.; Swarhing, D. J. In: Fluorine-Containing Molecules.

Structure, Reactivity, Synthesis and Applications; Liebman, J. F.; Greenberg,

A.; Dolbier, Jr., W. R., Eds.; VCH: New York, 1988; p 259.

[198] Bhattacharya, B. K.; Rao, T. S.; Revankar, G. R. Total synthesis of 2'-deoxy-

2'-arafluoro-tubercidin, -toyocamycin, -sangivamycin and certain related

nucleosides. J. Chem. Soc., Perkin Trans. 1, 1995, 1543-1550.

[199] Bhattacharya, B. K.; Ojwang, J. O.; Rando, R. F.; Huffman, J. H.; Revankar,

G. R. Synthesis and anti-DNA viral activities in vitro of certain 2,4-

disubstituted-7-(2-deoxy-2-fluoro- -D-arabinofuranosyl)pyrrolo[2,3-

d]pyrimidine nucleosides. J. Med. Chem., 1995, 38(20), 3957-3966.

[200] Ojwang, J. O.; Bhattacharya, B. K.; Marshall, H. B.; Korba, B. E.; Revankar,

G. R.; Rando, R. F. Inhibition of episomal hepatitis B virus DNA in vitro by

2,4-diamino-7-(2-deoxy-2-fluoro- -D-arabinofuranosyl)-pyrrolo[2,3-

d]pyrimidine. Antimicrob. Agents Chemother., 1995, 39(11), 2570-2573.

[201] Howell, H. G.; Brodfuehrer, P. R.; Brundidge, S. P.; Benigni, D. A.; Sapino,

Jr., C. Antiviral nucleosides. A stereospecific, total synthesis of 2'-fluoro-2'-

deoxy- -D-arabinofuranosyl nucleosides. J. Org. Chem., 1988, 53(1), 85-88.

[202] Peng, X.; Seela, F. Halogenated 7-deazapurine nucleosides: stereoselective

synthesis and conformation of 2'-deoxy-2'-fluoro- -D-arabinonucleosides.

Org. Biomol. Chem., 2004, 2(19), 2838-2846.

[203] Krawczyk, S. H.; Nassiri, M. R.; Kucera, L. S.; Kern, E. R.; Ptak, R. G.;

Wotring, L. L.; Drach, J. C.; Townsend, L. B. Synthesis and antiproliferative

and antiviral activity of 2'-deoxy-2'-fluoroarabinofuranosyl analogs of the

nucleoside antibiotics toyocamycin and sangivamycin. J. Med. Chem., 1995,

38(20), 4106-4114.

[204] Ford, Jr., H.; Dai, F.; Mu, L.; Siddiqui, M. A.; Nicklaus, M. C.; Anderson,

L.; Marquez, V. E.; Barchi, Jr., J. J. Adenosine deaminase prefers a distinct

sugar ring conformation for binding and catalysis: kinetic and structural

studies. Biochemistry, 2000, 39(10), 2581-2592.

[205] Seela, F.; Xu, K.; Eickmeier, H. 2 -Deoxy-5-fluorotubercidin. Acta

Crystallogr., Sect. C: Cryst. Struct. Commun., 2005, 61(6), o408-o410.

[206] Seela, F.; Ding, P.; Peng, X.; Eickmeier, H.; Reuter, H. The 7-bromo

derivative of 2-amino-2 -deoxytubercidin fluorinated at the sugar moiety.

Acta Crystallogr., Sect. C: Cryst. Struct. Commun., 2007, 63(10), o600-o602.

[207] Seela, F.; Xu, K.; Eickmeier, H.; Reuter, H. Unpublished results. 2008.

[208] Eldrup, A. B.; Prhavc, M.; Brooks, J.; Bhat, B.; Prakash, T. P.; Song, Q.;

Bera, S.; Bhat, N.; Dande, P.; Cook, P. D.; Bennett, C. F.; Carroll, S. S.; Ball,

R. G.; Bosserman, M.; Burlein, C.; Colwell, L. F.; Fay, J. F.; Flores, O. A.;

Getty, K.; LaFemina, R. L.; Leone, J.; MacCoss, M.; McMasters, D. R.;

Tomassini, J. E.; von Langen, D.; Wolanski, B.; Olsen, D. B.

Structure activity relationship of heterobase-modified 2‘-C-methyl

ribonucleosides as inhibitors of hepatitis C virus RNA replication. J. Med.

Chem., 2004, 47(21), 5284-5297.

[209] Rosemeyer, H.; Seela, F. 2 , 3 -Dideoxy-3 -fluorotubercidin and related

dideoxyribonucleosides: synthesis via a 2 -deoxy-3 -oxoribofuranoside

intermediate and conformation studies. Helv. Chim. Acta, 1989, 72(5), 1084-

1094.

[210] Seela, F.; Muth, H.-P. 3 -Substituted and 2 ,3 -unsaturated 7-deazaguanine

2 ,3 -dideoxynucleosides: syntheses and inhibition of HIV-1 reverse

transcriptase. Helv. Chim. Acta, 1991, 74(5), 1081-1090.

[211] Seela, F.; Muth, H.-P. Synthesis of 4-substituted 2-aminopyrrolo-[2,3-

d]pyrimidine 2',3'-dideoxyribonucleosides. Liebigs Ann. Chem., 1990, 227-

232.

[212] Ludwig, J. A new route to nucleoside 5'-triphosphates. Acta Biochim.

Biophys. Acad. Sci. Hung., 1981, 16(3-4), 131-133.

[213] Atkinson, M. R.; Deutscher, M. P.; Kornberg, A.; Russell, A. F.; Moffatt, J.

G. Enzymatic synthesis of deoxyribonucleic acid. XXXIV. Termination of

chain growth by a 2',3'-dideoxyribonucleotide. Biochemistry, 1969, 8(12),

4897-4904.

[214] van der Vliet, P. C.; Kwant, M. M. Role of DNA polymerase in adenovirus

DNA replication. Mechanism of inhibition by 2',3'-dideoxynucleoside 5'-

triphosphates. Biochemistry, 1981, 20(9), 2628-2632.

[215] Waqar, M. A.; Evans, M. J.; Manly, K. F.; Hughes, R. G.; Huberman, J. A.

Effects of 2 ,3 -dideoxynucleosides on mammalian cells and viruses. J. Cell.

Physiol., 1984, 121(2), 402-408.

[216] Smoler, D.; Molineux, I.; Baltimore, D. Direction of polymerization by the

avian myeloblastosis virus deoxyribonucleic acid polymerase. J. Biol. Chem.,

1971, 246(24), 7697-7700.

[217] Mitsuya, H.; Broder, S. Inhibition of the in vitro infectivity and cytopathic

effect of human T-lymphotrophic virus type III/lymphadenopathy-associated

virus (HTLV-III/LAV) by 2',3'-dideoxynucleosides. Proc. Natl. Acad. Sci.

USA, 1986, 83(6), 1911-1915.

[218] De Clercq, E. Chemotherapeutic approaches to the treatment of the acquired

immune deficiency syndrome (AIDS). J. Med. Chem., 1986, 29(9), 1561-

1569.

[219] Seela, F.; Bourgeois, W.; Gumbiowski, R.; Mertens, A.; Muth, H.-P.; Röling,

A.; Rosemeyer, H. In: Progress in AIDS Research; Schauzu, M., Ed.; MMV

Medizin Verlag: München, 1990.

[220] Sanger, F.; Nicklen, S.; Coulson, A. R. DNA sequencing with chain-

terminating inhibitors. Proc. Natl. Acad. Sci. USA, 1977, 74(12), 5463-5467.


[221] Marziali, A.; Akeson, M. New DNA sequencing methods. Annu. Rev.

Biomed. Eng., 2001, 3(1), 195-223.

[222] Hobbs, Jr., J. F. W.; Coccuzza, A. J. Alkynylamino-nucleotides. U.S. Patent

5, 047, 519, Sep. 10, 1991.

[223] Smith, L. M.; Sanders, J. Z.; Kaiser, R. J.; Hughes, P.; Dodd, C.; Connell, C.

R.; Heiner, C.; Kent, S. B. H.; Hood, L. E. Fluorescence detection in

automated DNA sequence analysis. Nature, 1986, 321, 674-679.

[224] Swerdlow, H.; Zhang, J. Z.; Chen, D. Y.; Harke, H. R.; Grey, R.; Wu, S.;

Dovichi, N. J.; Fuller, C. Three DNA sequencing methods using capillary gel

electrophoresis and laser-induced fluorescence. Anal. Chem., 1991, 63(24),

2835-2841.

[225] Brazill, S. A.; Kim, P. H.; Kuhr, W. G. Capillary gel electrophoresis with

sinusoidal voltammetric detection: a strategy to allow four-“color” DNA

sequencing. Anal. Chem., 2001, 73(20), 4882-4890.

[226] Hobbs, Jr., F. W. Palladium-catalyzed synthesis of alkynylamino

nucleosides. A universal linker for nucleic acids. J. Org. Chem., 1989,

54(14), 3420-3422.

[227] Finn, P. J.; Bull, M. G.; Xiao, H.; Phillips, P. D.; Nelson, J. R.; Grossmann,

G.; Nampalli, S.; McArdle, B. F.; Mamone, J. A.; Flick, P. K.; Fuller, C. W.;

Kumar, S. Efficient incorporation of positively charged 2 ,3 -

dideoxynucleoside-5 -triphosphates by DNA polymerases and their

application in ‘direct-load’ DNA sequencing. Nucleic Acids Res., 2003,

31(16), 4769-4778.

[228] Edwards, J. R.; Itagaki, Y.; Ju, J. DNA sequencing using biotinylated

dideoxynucleotides and mass spectrometry. Nucleic Acids Res., 2001,

29(21), e104.

[229] Seela, F.; Muth, H.-P. Synthese von 7-Desaza-2',3'-didesoxyguanosin durch

Desoxygenierung seines 2'-Desoxy- -D-ribofuranosids. Liebigs Ann. Chem.,

1988, 215-219.

[230] Serafinowski, P. Synthesis of 2 ,3 -didehydro-2 ,3 -dideoxyformycin A, 2',3 -

dideoxyformycin A and 2 ,3 -dideoxytubercidin. Synthesis, 1990, 411-415.

[231] Seela, F.; Gumbiowski, R.; Muth, H.-P.; Bourgeois, W. Synthesis of

pyrrolo[2,3-b]pyridine nucleosides by solid-liquid phase-transfer

glycosylation and deoxygenation of 4-chloropyrrolo[2,3-d]pyrimidine 2 -

deoxyribofuranosides. Nucleosides Nucleotides, 1989, 8(5), 1087-1088.

[232] Serafinowski, P. Synthesis of some S-3 -deoxyadenosyl-L-homocysteine

analogues. Nucleic Acids Res., 1987, 15(3), 1121-1137.

[233] Okabe, M.; Sun, R.-C.; Tam, S. Y.-K.; Todaro, L. J.; Coffen, D. L. Synthesis

of the dideoxynucleosides ddC and CNT from glutamic acid, ribonolactone,

and pyrimidine bases. J. Org. Chem., 1988, 53(20), 4780-4786.

[234] Seela, F.; Rosemeyer, H.; Fischer, S. Synthesis of 3-deaza-2 -

deoxyadenosine and 3-deaza-2 ,3 -dideoxyadenosine: glycosylation of the 4-

chloroimidazo[4,5-c]pyridinyl anion. Helv. Chim. Acta, 1990, 73(6), 1602-

1611.

[235] Seela, F.; Muth, H.-P.; Röling, A. Syntheses of pyrrolo[2,3-d]pyrimidine

2 ,3 -dideoxyribonucleosides related to 2 ,3 -dideoxyadenosine and 2 ,3 -

dideoxyguanosine and inhibitory activity of 5 -triphosphates on HIV-1

reverse transcriptase. Helv. Chim. Acta, 1991, 74(3), 554-564.

[236] Seela, F.; Bourgeois, W.; Muth, H.-P.; Rosemeyer, H. Facile synthesis of

pyrrolo[2,3-d]pyrimidine and pyrrolo[3,2-c]pyridine 2',3'-dideoxyribo-

nucleosides via nucleobase anion glycosylation with 2,3-dideoxy-D-glycero-

pentofuranosyl chloride. Heterocycles, 1989 29(11), 2193-2197.

[237] Appel, R. Tertiary phosphane/tetrachloromethane, a versatile reagent for

chlorination, dehydration, and P-N linkage. Angew. Chem. Int. Ed., 1975,

14(12), 801-811.

[238] Wilcox, C. S.; Otoski, R. M. Stereoselective preparations of ribofuranosyl

chlorides and ribofuranosyl acetates. Solvent effects and stereoselectivity in

the reaction of ribofuranosyl acetates with trimethylallylsilane. Tetrahedron

Lett., 1986, 27(9), 1011-1014.

[239] Balzarini, J.; Pauwels, R.; Herdewijn, P.; De Clercq, E.; Cooney, D. A.;

Kang, G.-J.; Dalal, M.; Johns, D. G.; Broder, S. Potent and selective anti-

HTLV-III/LAV activity of 2',3'-dideoxycytidinene, the 2',3'-unsaturated

derivative of 2',3'-dideoxycytidine. Biochem. Biophys. Res. Commun., 1986,

140(2), 735-742.

[240] Baba, M.; Pauwels, R.; Herdewijn, P.; De Clercq, E.; Desmyter, J.;

Vandeputte, M. Both 2',3'-dideoxythymidine and its 2',3'-unsaturated

derivative (2',3'-dideoxythymidinene) are potent and selective inhibitors of

human immunodeficiency virus replication in vitro. Biochem. Biophys. Res.

Commun., 1987, 142(1), 128-134.

[241] Yarchoan, R.; Mitsuya, H.; Thomas, R. V.; Pluda, J. M.; Hartman, N. R.;

Perno, C.-F.; Marczyk, K. S.; Allain, J.-P.; Johns, D. G.; Broder, S. In vivo

activity against HIV and favorable toxicity profile of 2',3'-dideoxyinosine.

Science, 1989, 245, 412-415.

[242] Flückiger-Isler, R. E.; Walter, P. Stimulation of rat liver glycogen synthesis

by the adenosine kinase inhibitor 5-iodotubercidin. Biochem. J., 1993, 292,

85-91.

[243] Massillon, D.; Stalmans, W.; van de Werve, G.; Bollen, M. Identification of

the glycogenic compound 5-iodotubercidin as a general protein kinase

inhibitor. Biochem. J., 1994, 299, 123-128.

[244] Acton, E. M.; Ryan, K. J.; Goodman, L. Synthesis of L-ribofuranose and L-

adenosine. J. Am. Chem. Soc., 1964, 86(23), 5352-5354.

[245] Asai, M.; Hieda, H.; Shimizu, B. Studies on synthetic nucleotides. IV.

Preparation of L- -ribonucleosides and L- -ribonucleotides. Chem. Pharm.

Bull., 1967, 15(12), 1863-1870.

[246] Hol , A.; orm, F. Preparation of some O-L-ribonucleosides. Collect. Czech.

Chem. Commun., 1969, 34, 3383-3401.

[247] Wang, P.; Hong, J. H.; Cooperwood, J. S.; Chu, C. K. Recent advances in L-

nucleosides: chemistry and biology. Antiviral Res., 1998, 40, 19-44.

[248] Gumina, G.; Song, G.-Y.; Chu, C. K. L-Nucleosides as chemotherapeutic

agents. FEMS Microbiol. Lett., 2001, 202(1), 9-15.

[249] Gumina, G.; Chong, Y.; Choo, H.; Song, G.-Y.; Chu, C. K. L-Nucleosides:

antiviral activity and molecular mechanism. Curr. Top. Med. Chem., 2002, 2,

1065-1086.

[250] Bryant, M. L.; Bridges, E. G.; Placidi, L.; Faraj, A.; Loi, A.-G.; Pierra, C.;

Dukhan, D.; Gosselin, G.; Imbach, J.-L.; Hernandez, B.; Juodawlkis, A.;

Tennant, B.; Korba, B.; Cote, P.; Marion, P.; Cretton-Scott, E.; Schinazi, R.

F.; Sommadossi, J.-P. Antiviral L-nucleosides specific for hepatitis B virus

infection. Antimicrob. Agents Chemother., 2001, 45(1), 229-235.

[251] Seela, F.; Lin, W.; Kazimierczuk, Z.; Rosemeyer, H.; Glaçon, V.; Peng, X.;

He, Y.; Ming, X.; Andrzejewska, M.; Gorska, A.; Zhang, X.; Eickmeier, H.;

La Colla, P. L-Nucleosides containing modified nucleobases. Nucleosides

Nucleotides Nucleic Acids, 2005, 24(5), 859-863.

[252] Zemlicka, J. Enantioselectivity of the antiviral effects of nucleoside

analogues. Pharmacol. Ther., 2000, 85(3), 251-266.

[253] Graciet, J.-C. G.; Schinazi, R. F. In: Advances in Antiviral Drug Design; De

Clercq, E., Ed.; Elsevier Science B. V.: 1999; Vol. 3.

[254] Rolland, V.; Kotera, M.; Lhomme, J. Convenient preparation of 2-deoxy-3,5-

di-O-p-toluoyl- -D-erythro-pentofuranosyl chloride. Synth. Commun., 1997,

27(20), 3505-3511.

[255] Seela, F.; Peng, X. Pyrrolo[2,3-d]pyrimidine -L-nucleosides containing 7-

deazaadenine, 2-amino-7-deazaadenine, 7-deazaguanine, 7-deazaisoguanine,

and 7-deazaxanthine. Collect. Czech. Chem. Commun., 2006, 71, 956-977.

[256] Seela, F.; Peng, X. 7-Functionalized 7-deazapurine ribonucleosides related to

2-aminoadenosine, guanosine, and xanthosine: glycosylation of pyrrolo[2,3-

d]pyrimidines with 1-O-acetyl-2,3,5-tri-O-benzoyl-D-ribofuranose. J. Org.

Chem., 2006, 71(1), 81-90.

[257] Girgis, N. S.; Michael, M. A.; Smee, D. F.; Alaghamandan, H. A.; Robins, R.

K.; Cottam, H. B. Direct C-glycosylation of guanine analogs: the synthesis

and antiviral activity of certain 7- and 9-deazaguanine C-nucleosides. J. Med.

Chem., 1990, 33(10), 2750-2755.

[258] Seela, F.; Debelak, H. The C8-(2‘-deoxy- -D-ribofuranoside) of 7-

deazaguanine: synthesis and base pairing of oligonucleotides with unusually

linked nucleobases. J. Org. Chem., 2001, 66(10), 3303-3312.

[259] Ti, G. S.; Gaffney, B. L.; Jones, R. A. Transient protection: efficient one-

flask syntheses of protected deoxynucleosides. J. Am. Chem. Soc., 1982,

104(5), 1316-1319.

[260] Inoue, H.; Imura, A.; Ohtsuka, E. Synthesis of dodecadeoxyribonucleotides

containing a pyrrolo[2,3-d]pyrimidine nucleoside and their base-pairing

ability. Nippon Kagaku Kaishi, 1987, 7, 1214-1220.

[261] Woo, J.; Meyer, Jr., R. B.; Gamper, H. B. G/C-modified oligodeoxy-

nucleotides with selective complementarity: synthesis and hybridization

properties. Nucleic Acids Res., 1996, 24(13), 2470-2475.

[262] Barr, P. J.; Jones, A. S.; Serafinowski, P.; Walker, R. T. The synthesis of

nucleosides derived from 5-ethynyluracil and 5-ethynylcytosine. J. Chem.

Soc., Perkin Trans. 1, 1978, 1263-1267.

[263] Robins, M. J.; Barr, P. J. Nucleic acid related compounds. 39. Efficient

conversion of 5-iodo to 5-alkynyl and derived 5-substituted uracil bases and

nucleosides. J. Org. Chem., 1983, 48(11), 1854-1862.

[264] Sniady, A.; Durham, A.; Morreale, M. S.; Marcinek, A.; Szafert, S.; Lis, T.;

Brzezinska, K. R.; Iwasaki, T.; Ohshima, T.; Mashima, K.; Dembinski, R.

Zinc-catalyzed cycloisomerizations. Synthesis of substituted furans and

furopyrimidine nucleosides. J. Org. Chem., 2008, 73(15), 5881-5889.

[265] Seela, F.; Sirivolu, V. R. Pyrrolo-dC oligonucleotides bearing alkynyl side

chains with terminal triple bonds: synthesis, base pairing and fluorescent dye

conjugates prepared by the azide-alkyne "click" reaction. Org. Biomol.

Chem., 2008, 6(9), 1674-1687.

[266] Berry, D. A.; Jung, K.-Y.; Wise, D. S.; Sercel, A. D.; Pearson, W. H.;

Mackie, H.; Randolph, J. B.; Somers, R. L. Pyrrolo-dC and pyrrolo-C:

fluorescent analogs of cytidine and 2'-deoxycytidine for the study of

oligonucleotides. Tetrahedron Lett., 2004, 45(11), 2457-2461.

[267] Loakes, D.; Brown, D. M.; Salisbury, S. A.; McDougall, M. G.; Neagu, C.;

Nampalli, S.; Kumar, S. Synthesis and some biochemical properties of a

novel 5,6,7,8-tetrahydropyrimido[4,5-c]pyridazine nucleoside. Helv. Chim.

Acta, 2003, 86(4), 1193-1204.

[268] Robins, M. J.; Miranda, K.; Rajwanshi, V. K.; Peterson, M. A.; Andrei, G.;

Snoeck, R.; De Clercq, E.; Balzarini, J. Synthesis and biological evaluation

of 6-(alkyn-1-yl)furo[2,3-d] pyrimidin-2(3H)-one base and nucleoside

derivatives. J. Med. Chem., 2005, 49(1), 391-398.

[269] Srinivasan, S.; McGuigan, C.; Andrei, G.; Snoeck, R.; De Clercq, E.;

Balzarini, J. Bicyclic nucleoside inhibitors of varicella-zoster virus (VZV):

the effect of terminal unsaturation in the side chain. Biorg. Med. Chem. Lett.,

2001, 11(3), 391-393.

[270] Koh, Y.-H.; Shim, J. H.; Girardet, J.-L.; Hong, Z. Design and evaluation of a

potential mutagen for Hepatitis C virus. Biorg. Med. Chem. Lett., 2007,

17(18), 5261-5264.

[271] Leonard, P.; Ingale, S. A.; Ding, P.; Ming, X.; Seela, F. Studies on the

glycosylation of pyrrolo[2,3-d]pyrimidines with 1-O-acetyl-2,3,5-tri-O-

benzoyl- -D-ribofuranose: the formation of regioisomers during


toyocamycin and 7-deazainosine syntheses. Nucleosides Nucleotides Nucleic

Acids, 2009, 28(5), 678-694.

[272] Saito, Y.; Shinohara, Y.; Bag, S. S.; Takeuchi, Y.; Matsumoto, K.; Saito, I.

Ends free and self-quenched molecular beacon with pyrene labeled

pyrrolocytidine in the middle of the stem. Tetrahedron, 2009, 65(4), 934-

939.

[273] Hudson, R. H. E.; Ghorbani-Choghamarani, A. Selective fluorometric

detection of guanosine-containing sequences by 6-phenylpyrrolocytidine in

DNA. Synlett, 2007, 870-873.

[274] Hudson, R. H. E.; Choghamarani, A. G. The 6-methoxymethyl derivative of

pyrrolo-dC for selective fluorometric detection of guanosine-containing

sequences. Nucleosides Nucleotides Nucleic Acids, 2007, 26(6), 533-537.

[275] Aucagne, V.; Amblard, F.; Agrofoglio, L. A. Highly efficient AgNO3-

catalyzed preparation of substituted furanopyrimidine nucleosides. Synlett,

2004, 2406-2408.

[276] Ranasinghe, R. T.; Rusling, D. A.; Powers, V. E. C.; Fox, K. R.; Brown, T.

Recognition of CG inversions in DNA triple helices by methylated 3H-

pyrrolo[2,3-d]pyrimidin-2(7H)-one nucleoside analogues. Chem. Commun.,

2005, 2555-2557.

[277] Liu, C.; Martin, C. T. Fluorescence characterization of the transcription

bubble in elongation complexes of T7 RNA polymerase. J. Mol. Biol., 2001,

308(3), 465-475.

[278] Lin, K.-Y.; Matteucci, M. D. A cytosine analogue capable of clamp-like

binding to a guanine in helical nucleic acids. J. Am. Chem. Soc., 1998,

120(33), 8531-8532.

[279] Flanagan, W. M.; Wolf, J. J.; Olson, P.; Grant, D.; Lin, K.-Y.; Wagner, R.

W.; Matteucci, M. D. A cytosine analog that confers enhanced potency to

antisense oligonucleotides. Proc. Natl. Acad. Sci. USA, 1999, 96(7), 3513-

3518.

[280] Gerrard, S. R.; Srinivasan, N.; Fox, K. R.; Brown, T. CG Base pair

recognition within DNA triple helices using N-methyl-3H-pyrrolo[2,3-

d]pyrimidin-2(7H)-one nucleoside analogues. Nucleosides Nucleotides

Nucleic Acids, 2007, 26(10), 1363-1367.

[281] Gerrard, S. R.; Edrees, M. M.; Bouamaied, I.; Fox, K. R.; Brown, T. CG base

pair recognition within DNA triple helices by modified N-methylpyrrolo-dC

nucleosides. Org. Biomol. Chem., 2010, 8(22), 5087-5096.

[282] Lin, K.-Y.; Jones, R. J.; Matteucci, M. Tricyclic 2'-deoxycytidine analogs:

syntheses and incorporation into oligodeoxynucleotides which have

enhanced binding to complementary RNA. J. Am. Chem. Soc., 1995,

117(13), 3873-3874.

[283] Ausín, C.; Ortega, J.-A.; Robles, J.; Grandas, A.; Pedroso, E. Synthesis of

amino- and guanidino-G-clamp PNA monomers. Org. Lett., 2002, 4(23),

4073-4075.

[284] Nakagawa, O.; Ono, S.; Li, Z.; Tsujimoto, A.; Sasaki, S. Specific fluorescent

probe for 8-oxoguanosine. Angew. Chem. Int. Ed., 2007, 46(24), 4500-4503.

[285] Holmes, S. C.; Arzumanov, A. A.; Gait, M. J. Steric inhibition of human

immunodeficiency virus type-1 Tat-dependent trans-activation in vitro and in

cells by oligonucleotides containing 2 -O-methyl G-clamp ribonucleoside

analogues. Nucleic Acids Res., 2003, 31(11), 2759-2768.

[286] Seela, F.; Wei, C. 7-Deazaisoguanine quartets: self-assembled oligonucleo-

tides lacking the Hoogsteen motif. Chem. Commun., 1997, 1869-1870.

[287] Li, H.; Seela, F. Unpublished results. 2006.

[288] Seela, F.; Kröschel, R. Quadruplex and pentaplex self-assemblies of

oligonucleotides containing short runs of 8-aza-7-deaza-2‘-deoxyisoguano-

sine or 2‘-deoxyisoguanosine. Bioconjugate Chem., 2001, 12(6), 1043-1050.

[289] Taylor, E. C.; Kuhnt, D.; Shih, C.; Rinzel, S. M.; Grindey, G. B.; Barredo, J.;

Jannatipour, M.; Moran, R. G. A dideazatetrahydrofolate analog lacking a

chiral center at C-6, N-[4-[2-(2-amino-3,4-dihydro-4-oxo-7H-pyrrolo[2,3-

d]pyrimidin-5-yl)ethyl]benzoyl]-L-glutamic acid, is an inhibitor of thymi-

dylate synthase. J. Med. Chem., 1992, 35(23), 4450-4454.

[290] Kawai, K.; Kodera, H.; Osakada, Y.; Majima, T. Sequence-independent and

rapid long-range charge transfer through DNA. Nat. Chem., 2009, 1(2), 156-

159.

Received: 09 December, 2010 Revised: 02 May, 2011 Accepted: 05 August, 2011

7-deazapurine (pyrrolo[2,3- d]pyrimidine) 2 ... organic chemistry, 2012, 16, 161-223 161...

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