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Nucleic Acid Structure
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• Objectives:
To know and identify the structure, roles and classifications of
• bases• sugars• nucleosides• nucleotides• DNAs• RNAs
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Bases
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Nucleic Acids / Bases/Structure
Pyrimidine
Imidazole
By the attachment of differentBy the attachment of different
groups to the rings, different typesgroups to the rings, different types
of Py and Pu are generated.of Py and Pu are generated.
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Structures of the nitrogenous bases in DNA and RNA
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NA / Bases/ Classification
• Purine Bases (pu): Purine Bases (pu): • Major : (A)&(G)Major : (A)&(G)• Minor: Inosine(I) & Minor: Inosine(I) & methyl guanine(7mG) methyl guanine(7mG) • Unnatural : Unnatural :
MercaptopurineMercaptopurine,,
Allopurinol & Allopurinol &
8-Azaguanine 8-Azaguanine
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• Pyrimidines (py): Pyrimidines (py):
• Major : (T), (C) & (U) Major : (T), (C) & (U)
•Minor: DHU , 5mC & 5hmCMinor: DHU , 5mC & 5hmC
•Unnatural: Fluorouracil (5FU) & Unnatural: Fluorouracil (5FU) & 6-aza cytosine( AZC) 6-aza cytosine( AZC)
NA / Bases/ Classification/ Py
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NA / Bases/ Isomerism/ Tautomerism
Diffinition:Diffinition: is a kind is a kind of isomerism between of isomerism between amine-imine or keto amine-imine or keto (oxo)- enol groups.(oxo)- enol groups.
Types:Types: Lactam( Keto, Amine) Lactam( Keto, Amine) Lactyme (Enol, Imine)Lactyme (Enol, Imine)
Properties:Properties: They They have different have different hydrogen bonding hydrogen bonding patternspatterns
Physiologic Types:Physiologic Types: amino and oxo forms amino and oxo forms
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Sugars
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Nucleic Acids / Sugars
D-family
Aldo pentose
Furanose
β-Anomer
Ribose or deoxy Ribose
Numbered by Prime
Isomerism ( 2’ endo in DNA , 3’ endo in RNA)
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Structures of deoxyribose and ribose in DNA and RNA
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Nucleosides
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Nucleic Acids / Nucleosides
Structure :
Isomerism :
Nomenclature:
Roles :
Classification:
• β-N-glycosidic linkage of a base and a
pentose (1‘ to 9 in PU and 1‘ to
1 in PY).
• syn or anti conformation
• Name of the base + suffix sine for Pus(adenosine & guanosine)
• dine for PYs (uridine & thymidine)
• They are major part of nucleosides.
• Synthetic forms are used as drugs (Cytarabin)
Major:: Cytidine & deoxy cytidine.
• There are 8 major nucleotides.
Minor : ribothymidine (rT) & psudouracil (ΨU).
Unnatural : Cytarabin.
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Nucleotides
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Building block
Coenzymes (NAD, FAD & Co-A)
Group transfer
Energy carrier ( ATP & GTP)
Regulatory roles: Drugs
• in lipid synthesis( CDP-acylglycerol)in lipid synthesis( CDP-acylglycerol)• in sugar synthesis( UDP-glucose)in sugar synthesis( UDP-glucose)• in protein synthesis(tRNA)in protein synthesis(tRNA)• methyl donor as methyl donor as SAM SAM
(S-adenosylmethionine)(S-adenosylmethionine)
NA/ Nucleosides/ Biomedical importance
•Second messenger for hormones (cAMP or GMP)•Allosteric regulator of many enzymes (ATP & AMP in metabolic pathways)
• Synthetic pu & py analogs that contain
• Halogens, thiols or additional nitrogen are
• employed in:• treatment of gout or Hyperuricemia• (Allopurinol)• Chemotherapy of cancer ( cytarabin)• AIDS treatment ( azathioprine)• Immunosuppression responses
during organ • transplantation ( azathioprine)
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Nucleic Acids / Nucleotides
Structure:Isomerism:Nomenclature:Roles:Classification:
• Nucleoside+ Phosphate group(s
=phospho ester of nucleosides• In most cases the phosphate
group is linked to the 5’ carbon.• They may have 1, 2,or 3
phosphate groups.They may have syn or anti conformation They may have syn or anti conformation
with with predominate anti conformerpredominate anti conformer..
1-Name of the nucleoside1-Name of the nucleoside
+ the number of phosphate group.+ the number of phosphate group.
2-Name of their corresponding acid2-Name of their corresponding acid
such as thymidylic or guanylic acid.such as thymidylic or guanylic acid.
• Building block• Coenzymes (NAD, FAD & Co-A)• Group transfer• Energy carrier ( ATP & GTP)• Regulatory roles: • Drugs
MajorMajor:: CMP, dCMP, CDP, CTPCMP, dCMP, CDP, CTP
There are 24 major nucleotidesThere are 24 major nucleotides
MinorMinor : : cAMP, cGMPcAMP, cGMP
UnnaturalUnnatural : : Cytarabin Cytarabin
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Nucleic Acid:1-DNA2-RNA
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Nucleic Acids /DNA/ Structure• Objectives To know and identify different levels of
DNA organization
1- Primary structure
2-Secondary structure
Different geometry of
base pairs & base steps
3- Higher order of DNA structure
in prokaryotes
in Eukaryotes
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2’-deoxyribose sugars
Phosphodiester linkages
Directional chain (5’ to 3’)
4 Bases
purines: adenine & guanine
pyrimidines: cytosine & thymine
DNA is a polymer of2’-deoxyribonucleotides
GCTAp
5’ end
3’ end
C
G
T
A
HO-CH2
O
H2N-C
C
C
HN
N
N
CH
C
O
N
O
O
O P O CH2
O
O
C
N
N
CHC
CH
NH2
NH2
C
CN
N
N
CH
C
NHC
O
O
O P O CH2
O
O-PO32
O
O
O P O CH2
O
N
CC
O
HN
CHCO
CH3
1’
2’3’
4’
5’
3’
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DNA / Different ways to show primary structure
5’ 3’
Primary structure is a huge linear polymer of dNTPs that are joined to each other by 5’-3’ PDE bonds.
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Different bonds and interactions in
• Covalent:
PDE bonds in the backbone
• Hydrogen: between complementary bases
• Hydrophobic (van der Waals)
between the stacked adjacent base pairs.
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Secondary structure of DNA / Different ways to show it
5’ 3’
3’ 5’
Secondary structure is formed by base pairing between two complementary strands. It may be B, A or Z form.
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DNA / Different secondary structures
• B (duplex)
• A (duplex)
• Z (duplex)
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B-form DNA consists of a right-handed double helix with antiparallel strands
34 Å (10 bp) per turn
major groove
minor groovemajor groove
minor
3.4 Å per bp
These dimensions are for DNA fibers. In solution, there are ~10.5 base-pairs per turn.
5’ 3’
5’3’
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Summary of the main structural features of B-form DNA
•Right-handed helix
•Two antiparallel strands held together by Watson-
Crick hydrogen bonds
•Pitch (repeat length) = 34 Å (3.4 nm)
•36o rotation between residues
•Helix diameter of 20 Å (2.0 nm)
•Wide major groove, narrow minor groove
•Chargaff’s Rules: A = T; G = C
•Charged phosphates
•Bases in anti configuration
•The strands separate at high temperatures
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dsDNA
ssDNAnucleotides
dA
dC
dG
dU
The absorbance of double-stranded DNA (dsDNA) at 260 nm is less than that of either single-stranded DNA (ssDNA) or the free bases. This is called “hypochromism.”
Double-stranded and single-stranded DNA differ in their optical absorption at 260 nm
100
80
60
40
20
0
% D
enat
ured
110100908070Temperature /
oC
40 50 70% GC60
The temperature at which this “denaturation” or “melting” occurs depends on the pH and salt concentration, and increases with the GC content of the DNA. (The curves drawn here are schematic.)
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2nd structure of DNA/ A- DNAG enerated by dehydration of B-DNA
It is more compact than B-DNA
Has 2 grooves
Has 11bp/turn
Is right handed
Has a pitch per turn of helix 28 Ao
Side and top view of A -DNA in
ball-and-stick and space filling representation
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2nd structure of DNA/ Z- DNA
• Alternative G -C sequences form this zigzag
form DNA
• Is more narrower than B-DNA
• Has one groove
• Has 12 bp/turn
• Is left handed
• The stacked bases are almost perpendicular
• Has a pitch per turn of helix 45.6 Ao
PDB
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Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
A possible nucleosome structure
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Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
Fig. 2.26 Nucleosomes connected together by linker DNA and H1 histone to produce
the “beads-on-a-string” extended form of chromatin
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Packaging of nucleosomes into the 30-nm chromatin fiber
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Model for the organization of 30-nm chromatin fiber into looped domains
that are anchored to a nonhistone protein chromosome scaffold
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The many different orders of chromatin packing that give rise to the highly
condensed metaphase chromosome
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Histon likes proteins
HU (heat unstable)
H-NS(Histon like Nucleotide Structuring)
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RNAs
tRNA
mRNA
rRNA
hnRNA(hetererogenous nuclear RNA)
SnRNA (Snurps)
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RNA• Objectives:
To know and identify: Primary, secondary and Tertiary
structure of RNA.Structure and function of tRNA. Structure and function of rRNA. Structure and function of mRNA.
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RNA is a polymer of ribonucleotides
ribose sugars
Phosphodiester linkages
Directional chain (5’ to 3’)
4 Bases
purines: adenine & guanine
pyrimidines: cytosine & uracil
GCUAC
G
U
A
5’ end
3’ end
1’
2’3’
4’
5’
3’
OH
HO-CH2
O
H2N-C
C
C
HN
N
N
CH
C
O
N
O
O
O P O CH2
O
O
C
N
N
CHC
CH
NH2
OH
O
O
O P O CH2
O
N
CHC
O
HN
CHCO
OH
NH2
C
CN
N
N
CH
C
NHC
O
O
O P O CH2
O
O-PO32
OH
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tRNA Structure 5’’ 3’
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DNA / General facts
Particular region bound to protein clearly depart from the standard conformation
• Has specific groove (s)• It is flexible about its long axis it
• It may be linear or circular
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d. The bases of the two strands are held together by hydrogen bonds between complementary bases (two for A-T pairs and three for G-C pairs). Individual H-bonds are relatively weak and so the strands can be separated (by heating, for example). Complementary base pairing means that the sequence of one strand dictates the sequence of the other strand.
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Palindromic* sequences (inverted repeats) in DNA or RNA can form hairpin or cruciform structures
inverted repeats in an antiparallel double helix
3’
5’
5’
3’
T G C G A T A C T C A T C G C A
A C G C T A T G A G T A G C G T
hairpin
C
A C
T
3’5’
TAGCGT
ATCGCA
T
G AG
C
A C
T
cruciform
3’5’
5’3’
TAGCGT
ATCGCA
TGCGAT
ACGCTA
Mirror repeats cannot form these structures.
*A palindrome reads the same in either direction (“Radar,” “Madam, I’m Adam”).
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DNA / General facts• Its structure was discovered in 1953 by Watson
and Crick• It is a polyester compound• Has acidic character
It is a polymer in which the monomers (nucleotides)are joined by PDE bonds between5’ and 3’ carbon atoms of two successive nucleotides.
Because of the phosphate
moiety, they have acidic
character (negatively charged).
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• Has polarity
• It is double helix
DNA / General facts
DNA has end-to-end
chemical Orientation
(3’ and 5’ ends) and
by convention it
is written in the
5’ 3’ direction
• The two strand are:
1- in opposite polarities
2- stabled by different bonds:
-Hydrophobic bond
-H bond
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RNA is easily hydrolyzed under alkaline conditions
The reaction proceeds through a 2’,3’-cyclic monophosphate intermediate. Enzymatic hydrolysis of RNA by RNase proceeds through a similar intermediate. Because DNA lacks the 2’-OH group, it is stable under alkaline conditions.
.
...
O P O-CH2
O
OO
N
OHO
O P O CH2
OO
N
OHO
O P O
O
...
OH
ON
OHO
O P O
O
...
HOCH2
O
.
...
O P O-CH2
O
O
N
OO
POO
H+
.
...
O P O-CH2
O
OO
N
OHO
O P OH
O
mixture of 2’- and 3’- monophosphate derivatives
H2O
shortened RNA
RNA
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What about DNA grooves
• They are generated because of the angle of base pairs
• They are important for the interaction with proteins
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2nd structure of DNA/ B- DNA• Is the abundant form• Has 2 groooves• Has 10 (10.5) bp/ turn• Is right handed• Has a pitch per turn of helix 34 Ao
Side and top view of B-DNA in ball-and-stick and space filling representation
The helix tilted 32˚ from the viewer to show minor (m) and major (M) grooves.