ars.els-cdn.com · web viewfigure s3 thermal melting curves of triplexes formed between tfo2 and hp...
TRANSCRIPT
Supporting Information
The ability of a triplex-forming oligonucleotide to recognize T-A and C-G base pairs in a DNA duplex is enhanced by incorporating N-acetyl-2,7-diaminoquinoline
Akihiro Ohkubo, Tatsuya Ohnishi, Shuhei Nishizawa, Yuri Nishimura, Shugo Hisamatsu
Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
Corresponding Authors* E-mail: [email protected]
Corresponding author. Tel.: + 81-45-924-5828; fax: +81-45-924-5828; e-mail: [email protected]
Figure S1 Chemical structure of the DANac phosphoramidite unit.
Figure S2. Measurement of the UV absorbance of compound 9 or 10 under varying pH conditions (pH 2.0-6.2). The measurements were carried out in a buffer containing 200 mM sodium citrate (pH 2.0-6.2) and 25 µM of each nucleoside.
Table S1. Comparison of the stabilities of triplexes formed between HP DNAs 1-4 and TFO 1-2. Tm
measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 7.4-6.0), 100 mM NaCl, 10 mM MgCl2, 0.5 mM spermine, and 1.5 µM triplex DNA.The values represent the mean ± SEM for three separate experiments.
- S2 -
Figure S3 Thermal melting curves of triplexes formed between TFO2 and HP DNA 1, 2, and 5. The measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 7. 0), 100 mM NaCl, 10 mM MgCl2, 0.5 mM spermine, and 1.5 µM triplex DNA.
- S3 -
Figure S4. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 1. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 7.4), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA.
Figure S5. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 1. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 7.0), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA.
Figure S6. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 1. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 6.4), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA.
- S4 -
Figure S7. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 1. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 6.0), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA.
Figure S8. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 2. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 7.4), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA.
Figure S9. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 2. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 7.0), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA.
- S5 -
Figure S10. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 2. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 6.4), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA.
Figure S11. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 2. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 6.0), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA.
Figure S12. Thermal melting curves of triplexes formed between HP DNAs 1-4 and TFO 5. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 7.0), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM triplex DNA
- S6 -
Figure S13. Thermal melting curves of triplexes formed between ODNs 2-5 and TFO 2. Tm measurements were carried out in a buffer containing 10 mM sodium cacodylate (pH 7.0), 100 mM NaCl, 10 mM MgCl 2, 0.5 mM spermine, and 1.5 µM duplex DNA.
- S7 -
Synthesis of compound 21H-NMR
- S8 -
13C NMR
HR-ESIMS
- S9 -
Synthesis of compound 31H-NMR
- S10 -
13C NMR
HR-ESIMS
- S11 -
Synthesis of compound 5 1H NMR
- S12 -
13C NMR
HR-ESIMS
- S13 -
Synthesis of compound 61H NMR
- S14 -
13C NMR
HR-ESIMS
- S15 -
Synthesis of compound 71H NMR
- S16 -
13C NMR
- S17 -
31P NMR
HR-ESIMS
- S18 -
Synthesis of compound 9 1H NMR
- S19 -
13C NMR
HR-ESIMS
- S20 -
Synthesis of compound 101H NMR
- S21 -
13C NMR
HR-ESIMS
- S22 -
Oligonucleotide SynthesisTFO 1: MALDI-TOF mass [M+H]+ calcd for [C183H237N42O120P17]+ : 5472.6, found : 5472.6
anion-exchange HPLC profile of TFO 1
5472.630
2737.453
5611.623
5287.837
DN
Ac-control-zip- 0:J2 M
S, Smoothed
0.0
0.5
1.0
1.5 4x10
Intens. [a.u.]
10002000
30004000
50006000
70008000
9000m
/z
- S23 -
TFO 2: MALDI-TOF mass [M+H]+ calcd for [C184H238N41O120P17]+ : 5471.7, found : 5472.3
anion-exchange HPLC profile of TFO 2
5472.342
2725.093
5610.681
TFO
-02-zip- 0:K17 M
S, Smoothed
0.0
0.5
1.0
1.5 4x10
Intens. [a.u.]
10002000
30004000
50006000
70008000
9000m
/z
- S24 -
TFO 3: MALDI-TOF mass [M+H]+ calcd for [C200H252N43O120P17]+ : 5706.0, found : 5706.2
anion-exchange HPLC profile of TFO 3
5706.185
2854.104
5844.426
2923 .898
DN
Ac-03-zip- 0:J3 M
S, Smoothed
0.0
0.5
1.0
1.5
2.0 4x10
Intens. [a.u.]
10002000
30004000
50006000
70008000
9000m
/z
- S25 -
TFO 4: MALDI-TOF mass [M+H]+ calcd for [C200H252N43O120P17]+ : 5706.0, found : 5706.4
anion-exchange HPLC profile of TFO 4
5706.419
2853.000
5844.682
3077.696
2773.308
3671.679
5457.820
3896.375
4200.757
2468.624
DA
QA
c-TFO
-04-zip- 0:D21 M
S, Smoothed
0.0
0.5
1.0
1.5
2.0
2.5 4x10
Intens. [a.u.]
10002000
30004000
50006000
70008000
9000m
/z
- S26 -
TFO 5: MALDI-TOF mass [M+H]+ calcd for [C188H246N41O137P17]+ : 5799.8, found : 5799.9
anion-exchange HPLC profile of TFO 5
5799.848
2899.518
3966.802
5939.104
1982.900
5403.987
4434.134
DAQAc-TFO-01-zip- 0:E16 MS, Smoothed
0.00
0.25
0.50
0.75
1.00
1.25 4x10
Intens. [a.u.]
10002000
30004000
50006000
70008000
9000m
/z
- S27 -