Molecules 2014, 19
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Et3N) to give Compound 4 (239 mg, 88%) as an orange foam: IR (KBr): ν 3437, 3410(NH, OH), 1701
(C=O), 1272 (N=N) cm−1; αD24 36.2 (c 1.00, CHCl3); H-NMR (500 MHz, CDCl3): δ 8.51 (1H, brs,
1
NH), 8.29 (1H, s, H-6), 7.90 (2H, d, J = 7.5 Hz), 7.70 (2H, d, J = 8.5 Hz), 7.52–7.45 (5H, m), 7.37–7.28
(6H, m), 7.16 (1H, dd, J = 6.5 and 1.0 Hz), 7.10 (2H, d, J = 8.0 Hz), 6.82–6.79 (4H, m) 6.38 (1H, dd,
J = 7.5, 6.5 Hz, H-1'), 4.60–4.59 (1H, m, H-3'), 4.14–4.13 (1H, m, H-4'), 3.70 (3H, s,OMe), 3.69 (3H,
s, OMe), 3.50 (1H, dd, J = 8.0 and 3.0 Hz, H-5'), 3.34 (1H, dd, J = 8.0 and 3.0 Hz, H-5'), 2.57–2.53
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(1H, m, H-2'), 2.40–2.34 (1H, m, H-2'), 2.09 (1H, brs, OH); C-NMR (125 MHz, CDCl3): δ 158.6,
152.6, 151.7, 148.8, 144.3, 135.4, 132.4, 131.3, 129.9, 129.1, 128.1, 127.9, 127.1, 125.1, 122.9, 122.5,
113.4, 100.4, 93.6, 87.2, 86.7, 85.9, 82.2, 72.4, 63.3, 55.2, 41.7; FAB-LRMS m/z = 757 (MNa+);
FAB-HRMS calcd for C44H38N4O7Na 757.2633, found 757.2633.
3.4. Preparation of 3-O-{2-Cyanoethyl(diisopropylamino)phosphino}-5'-O-(4,4'-Dimethoxytrityl)-5-
(4-phenyldiazenylphenyl)ethynyl-2'-deoxyuridine (5)
To a solution of compound 4 (188 mg, 0.26 mmol) in dry MeCN (5 mL) was added N,N-
diisopropylamine (0.13 mL,0.76 mmol) and 2-cyanoethyl-N,N'-diisopropylchlorophosphoramidite
(0.09 mL, 0.40mmol) at room temperature, and the reaction mixture was stirred for 1.5 h. The resultant
mixture was partitioned between AcOEt and H2O. The separated organic layer was washed with
saturated aqueous NaHCO3, followed by brine. The organic layer was dried (Na2SO4) and concentrated
in vacuo. The residue was purified by silica gel column chromatography and eluted with CHCl3/MeOH
(20:1 with 0.5% Et3N), to give a 17:3 diastereomeric mixture of 5 (324 mg, 82%) as an orange foam: IR
(KBr): ν 3610 (NH), 1699 (C=O), 1272 (N=N) cm−1; αD24 32.5 (c 1.00, CHCl3); H-NMR (500 MHz,
1
CDCl3): δ 9.08 (1H, brs, NH), 8.35 (0.85H, s, H-6), 8.30 (0.15H, s, H-6), 7.89 (2H, d, J = 7.5 Hz), 7.67
(2H, d, J = 8.5 Hz), 7.55–7.04 (14H, m), , 6.67–6.75 (4H, m), , 6.35 (1H, dd, J = 7.5, 6.0 Hz, H-1'),
4.68–4.61 (1H, m, H-3'), 4.26 (1H,m, H-4'), 3.70 (3H, s, OMe), 3.69 (3H, s, OMe), 3.67–3.53 (5H, m,
CH2CH2CN, H-5'), 3.31 (1H, dd, J = 8.5, 2.5 Hz, H-5'), 2.65–2.56 (1H, m, H-2'), 2.47–2.36 (3H, m,
H-2', ((CH3)2CH)2N), 1.18 (12H, d, J = 6.5 Hz, ((CH3)2CH)2N); 13C-NMR (125 MHz, CDCl3): δ
161.2, 158.5(9), 158.5(6), 152.6, 151.5, 149.1, 144.35, 142.5, 135.4, 132.3, 132.0, 131.1, 130.0 (d,
J (C, P) = 6.0 Hz), 129.1, 128.7, 128.0, 127.9 ,127.0, 125.1, 122.8, 122.4, 120.5, 117.3, 113.3, 100.3,
93.4, 86.3 (d, J (C, P) = 3.5 Hz), 85.9, 82.4, 77.3, 77.0, 76.8, 73.4, 73.2, 63.0, 58.2, 58.1, 55.1, 43.2 (d,
J (C, P) = 13.0 Hz), 40.8 (d, J (C, P) = 5.0 Hz), 25.6, 24.5(9), 24.5(3), 24.4(8), 20.2 (d, J (C, P ) = 7.0 Hz);
31P-NMR (200 MHz, CDCl3): δ 149.09, 148.66; FAB-LRMS m/z = 957 (MNa+); FAB-HRMS calcd
for C53H55N6O8PNa 957.3711, found 957.3711.
3.5. Synthesis of dUAz-Modified Oligodeoxynucleotides
Solid-phase oligonucleotide synthesis was performed on an nS-8 Oligonucleotides Synthesizer
(GeneDesign, Inc., Osaka, Japan) using commercially available reagents and phosphoramidites with
5-(bis-3, 5-trifluoromethylphenyl)-1H-tetrazole (0.25 M concentration in acetonitrile) as the activator.
dUAz phosphoramidite was chemically synthesized as described above. All of the reagents were
assembled, and the oligonucleotides were synthesized according to the standard synthesis cycle (trityl
on mode). Cleavage from the solid support and deprotection were accomplished with concentrated
ammonium hydroxide solution at 55 °C for 12 h. The crude oligonucleotides were purified with