Synthesis and Properties of Oligonucleotides
A R T I C L E S
THF, 1.06 mmol). The reaction was stirred at room temperature for
1.5 h, after which time the solvent was removed under reduced pressure.
Purification by flash chromatography on silica, eluting with 10%
methanol in methylene chloride containing 1% NH3, gave 14 (190 mg,
methylene chloride (3 mL) was added 2-cyanoethyl tetraisopropylphos-
phorodiamidite (0.028 mL, 0.085 mmol). The reaction was stirred for
1.5 h, after which time the solvent was removed under reduced pressure
and the residue was purified by flash chromatography on silica, eluting
with 4% methanol in methylene chloride containing 0.5% triethylamine,
90% yield) as a light green solid. mp 250 °C (dec); [R]23 +16° (c
D
1
0.55, MeOH:CHCl3 )1:1); H NMR (DMSO-d6) δ 11.05 (br s, 1H),
to give 25 (85 mg, 95% yield) as a yellow solid. mp 135 °C; [R]23
D
1
8.77 (dd, J ) 4.2, 1.7, 1H), 8.66 (d, J ) 8.3, 1H), 7.88 (d, J ) 8.9,
1H), 7.77 (d, J ) 8.9, 1H), 7.57 (dd, J ) 8.4, 4.2, 1H), 6.53-6.49 (m,
3H), 4.52-4.49 (m, 1H), 3.83-3.79 (m, 1H), 3.75 (s, 3H), 3.69 (dd, J
) 11.5, 5.2, 1H), 3.54 (dd, J ) 11.5, 5.6, 1H), 3.37-3.30 (m, 1H),
2.10-2.04 (m, 1H); 13C NMR (DMSO-d6) δ 154.11, 153.38, 152.81,
149.19, 148.60, 147.78, 144.55, 130.68, 129.11, 128.46, 121.75, 120.80,
117.73, 113.17, 104.05, 87.40, 81.94, 71.32, 62.34, 35.86, 28.58; HRMS
(FAB, NBA) m/z calcd for C21H22O4N9 (M + H) 464.1795, found
464.1806.
+55.8° (c 1.0, CH2Cl2); IR (KBr) 3408, 2964, 1625, 1530, 1340; H
NMR (CD2Cl2) δ 9.23 (s, 1H), 8.84 (dd, J ) 4.14, 1.66, 1H), 8.76 (d,
J ) 8.46, 1H), 8.49 (d, J ) 8.30, 1H), 7.91 (d, J ) 8.87, 1H), 7.61
(dd, J ) 8.92, 1.91, 1H), 7.48 (q, J ) 8.40, 4.18, 1H), 7.38 (t, J )
7.07, 2H), 7.26 (t, J ) 8.47, 4H), 7.19-7.11 (m, 3H), 6.78-6.64 (m,
5H), 5.07-4.93 (m, 1H), 4.24-4.19 (m, 1H), 3.91-3.22 (m, 16H),
3.10 (s, 3H), 3.05 (s, 3H), 2.60-2.57 (m, 4H), 1.34-1.07 (m, 12H);
13C NMR (CD2Cl2) δ 159.28, 159.25, 159.22, 159.19, 159.31, 156.22,
155.61, 155.54, 153.89, 153.83, 152.30, 152.26, 149.20, 149.00, 145.86,
145.80, 136.80, 136.66, 130.83, 130.78, 130.67, 130.61, 130.30, 128.93,
128.84, 128.47, 128.43, 128.36, 127.44, 127.36, 123.91, 123.85, 121.54,
118.50, 117.85, 117.79, 113.69, 112.81, 112.61, 112.42, 86.82, 86.78,
85.42, 82.84, 82.60, 75.89, 75.63, 74.92, 74.65, 65.27, 64.82, 59.38,
59.16, 59.01, 58.77, 55.88, 55.84, 55.79, 44.19, 44.02, 41.94, 41.90,
35.65, 29.20, 25.24, 25.15, 25.09, 25.00; HRMS (FAB NBA) m/z calcd
for C54H61N12O7P (M + H) 1021.4603, found 1021.4647.
N2-[(Dimethylamino)methylene]-8-[(3-methyl-3H-imidazo[4,5-f]-
quinolin-2-yl)amino]-â-D-2′-deoxyribofuranosyl]guanine (23). To a
stirred solution of 14 (100 mg, 0.22 mmol) in anhydrous methanol (5
mL) under an argon atmosphere was added N,N-dimethylformamide
diethyl acetal (0.3 mL, 1.76 mmol). The reaction was heated to 50 °C
and stirred for 2 h. The reaction mixture was allowed to cool to room
temperature, upon which time a precipitate formed. The precipitate was
collected by suction filtration and washed with cold methanol to give
General Procedure for the Buchwald-Hartwig Palladium-
Catalyzed Cross-Coupling Reaction of 20 with Simple Arylamines.
O6-Benzyl-8-(2-naphthalenylamino)-N9-[3′,5′-O-(1,1,3,3-tetrakis(iso-
propyl)-1,3-disiloxanediyl)-â-D-2′-deoxyribofuranosyl]guanine (26a).
2-Aminonaphthalene (44 mg, 0.303 mmol), Pd2(dba)3 (14 mg, 0.015
mmol), BINAP (28 mg, 0.0449 mmol), and 18 (100 mg, 0.147 mmol)
were placed in an oven-dried flask, and the flask was evacuated for 20
min and then filled with argon. Freshly distilled toluene (3 mL) was
degassed by bubbling a stream of argon through the solution for 5 min
and then was added to the flask, and the mixture was stirred for 15
min while maintaining an argon atmosphere. Lithium bis(trimethylsilyl)-
amide (1.0 M in THF, 0.3 mL, 0.30 mmol) was added, and the reaction
was heated to 100 °C for 30 min, and then cooled to room temperature
and quenched with saturated sodium bicarbonate (1 mL). The layers
were separated, and the aqueous phase was extracted with ethyl acetate.
The combined organic extracts were washed with 10% HCl and brine,
dried over sodium sulfate, filtered, and evaporated. Purification by flash
chromatography on silica, eluting with 18% ethyl acetate in hexanes,
23 (75 mg, 66% yield) as a light yellow solid. mp 280 °C (dec); [R]23
D
+12.4° (c 0.5, MeOH:CH2Cl2 ) 1:1); IR (KBr) 3346, 3220, 2924, 1666,
1
1629, 1601, 1544, 1493, 1348, 1283, 1112 cm-1; H NMR (DMSO-
d6) δ 8.81 (dd, J ) 4.16, 1.68, 1H), 8.69 (dd, J ) 4.64, 0.92, 1H), 8.43
(s, 1H), 7.86 (d, J ) 8.92, 1H), 7.78 (d, J ) 8.96, 1H), 7.58 (dd, J )
8.56, 4.16, 1H), 4.57-4.53 (m, 1H), 3.85-3.82 (m, 2H), 3.74 (s, 3H),
3.72-3.68 (m, 2H), 3.59-3.54 (m, 1H), 3.32-3.27 (m, 1H), 3.14 (s,
3H), 3.02 (s, 3H), 2.17-2.14 (m, 1H); 13C NMR (DMSO-d6) δ 158.18,
156.92, 154.33, 153.91, 150.08, 148.19, 147.59, 144.85, 130.05, 129.53,
128.64, 122.29, 121.20, 117.72, 113.48, 108.84, 87.63, 82.33, 71.55,
62.60, 55.27, 36.86, 34.94, 28.88; HRMS (FAB NBA) m/z calcd for
C24H26N10O4 (M+) 518.2138, found 518.2162.
N2-[(Dimethylamino)methylene]-8-[(3-methyl-3H-imidazo[4,5-f]-
quinolin-2-yl)amino]-N9[5′-O-[bis(4-methoxyphenyl)phenylmethyl]]-
â-D-2′-deoxyribofuranosyl]guanine (24). To a stirred solution of 23
(50 mg, 0.096 mmol) in anhydrous pyridine (1.0 mL) and freshly
distilled diisopropylethylamine (0.116 mL, 0.066 mmol) under an argon
atmosphere was added 4,4′-dimethoxytrityl chloride (98 mg, 0.29 mmol)
at 0 °C. After the addition, the reaction was allowed to warm to room
temperature and was stirred for 3 h. The solvent was then removed
under reduced pressure, and the residue was purified by flash chro-
matography on silica eluting with 1.0% methanol in methylene chloride
containing 0.5% triethylamine gave 24 (62 mg, 79% yield) as a light
yellow solid. mp 157° C (dec); [R]23D +37.6° (c 0.5, CH2Cl2); IR (KBr)
3397, 2927, 1626, 1531, 1340; 1H NMR (CD2Cl2) δ 9.31 (s, 1H), 8.81
(d, J ) 2.81, 2H), 8.77 (d, J ) 8.19, 1H), 8.37 (s, 1H), 7.84 (d, J )
8.78, 1H), 7.50 (d, J ) 8.87, 1H), 7.46 (dd, J ) 8.25, 3.94, 1H), 7.36
(d, J ) 7.92, 1.31, 2H), 7.24 (dd, J ) 7.73, 2.40, 4H), 7.14 (t, J )
7.80, 2H), 7.07 (t, J ) 7.25, 1H), 6.70-6.63 (m, 5H), 5.10 (q, J )
6.02, 3.88, 1H), 4.85 (q, J ) 7.02, 2.30, 1H), 3.71-3.65 (m, 2H), 3.62
(s, 3H), 3.58 (s, 3H), 3.51 (dd, J ) 0.024, 0.017, 1H), 3.43 (s, 3H),
3.29 (dd, J ) 9.62, 4.67, 1H), 3.03 (s, 3H), 2.97 (s, 3H), 2.47-2.41
(m, 1H); 13C NMR (CD2Cl2) δ 158.83, 158.78, 157.82, 155.55, 152.92,
151.89, 149.09, 148.47, 145.38, 145.16, 136.32, 136.27, 130.31, 130.17,
129.90, 128.40, 128.14, 128.01, 127.38, 126.98, 123.35, 121.13, 117.13,
113.24, 112.31, 86.41, 85.73, 82.40, 73.53, 65.29, 55.38, 41.51, 37.20,
35.16, 30.05, 28.50; HRMS (FAB NBA) m/z calcd for C45H44N10O6
(M + H) 821.3524, found 821.3552.
gave 26a (71 mg, 65% yield) as a yellow solid: mp 78-82 °C; [R]23
D
-44° (c 1.0, CHCl3); IR (KBr) 1680, 1589, 1364, 1038 cm-1; 1H NMR
(CDCl3) δ 8.12 (bs, 1H), 7.70-7.22 (m, 14H), 6.15 (dd, J ) 7.6, 3.8,
1H), 5.53 (s. 2H), 5.78 (dt, J ) 7.5, 7.3, 1H), 4.77 (s, 2H), 4.0-3.8
(m, 3H), 3.10 (m, 1H), 2.44-2.39 (m, 1H), 1.0-0.75 (m, 28H); 13C
NMR (CDCl3) δ 158.9, 158.3, 147.5, 183.1, 138.1, 135.0, 130.4, 129.1,
128.8, 127.9, 124.7, 120.6, 114.2, 113.1, 86.0, 84.9, 71.4, 68.6, 62.9,
39.5, 17.8, 17.6, 14.2, 13.5; HRMS (FAB, NBA) m/z calcd for
C39H53N6O5Si2 (M + H) 741.3616, found 741.3639.
O6-Benzyl-8-(9H-fluoren-2-ylamino)-N9-[3′,5′-O-(1,1,3,3-tetrakis-
(isopropyl)-1,3-disiloxanediyl)-â-D-2′-deoxyribofuranosyl]guanine
(26b). Obtained in 54% as a yellow solid: mp 95-97 °C; [R]23D -24°
(c 1.0, CHCl3); IR (KBr) 1680, 1591, 1462, 1038 cm-1 1H NMR
;
(CDCl3) δ 7.9 (bs, 1H), 7.67-7.21 (m, 16H), 6.21 (dd, J ) 8.7, 3.2,
1H), 5.58 (s, 2H), 4.79 (dt, J ) 7.1, 5.7, 1H), 4.63 (s, 2H), 4.12-3.87
(m, 6H), 3.04 (m, 1H), 2.46 (m, 1H), 1.08-0.69 (m, 28H); 13C NMR
(CDCl3) δ 158.9, 158.2, 154.1, 147.7, 145.3, 143.8, 142.4, 139.6, 137.8,
136.7, 129.2, 129.2, 128.8, 127.4, 126.5, 125.6, 120.8, 119.8, 118.1,
115.8, 113.1, 85.9, 84.8, 71.5, 68.5, 62.9, 39.4, 37.86, 18.1, 17.6, 14.2,
13.3; HRMS (FAB, NBA) m/z calcd for C42H55N6O5Si2 (M + H)
779.3772, found 779.3740.
N2-[(Dimethylamino)methylene]-8-[(3-methyl-3H-imidazo[4,5-f]-
quinolin-2-yl)amino]-N9-[5′-O-[bis(4-methoxyphenyl)phenylmethyl]-
3′-O-[[bis(1-methylethyl)amino](2-cyanoethoxy)phosphino]]-â-D-2′-
deoxyribofuranosyl]guanine (25). To a stirred suspension of 24 (50
mg, 0.061 mmol) and 1H-tetrazole (5 mg, 0.07 mmol) in anhydrous
O6-Benzyl-8-[(1,1′-biphenyl)-4-ylamino]-N9-[3′,5′-O-(1,1,3,3-tet-
rakis(isopropyl)-1,3-disiloxanediyl)-â-D-2′-deoxyribofuranosyl]gua-
nine (26c). Obtained in 62% yield as a yellow solid: mp 86-91 °C;
[R]23 -28° (c 1.0, CHCl3); IR (KBr) 1589, 1560, 1460, 1040 cm-1
;
D
1H NMR (CDCl3) δ 7.82-7.24 (m, 18H), 6.21 (dd, J ) 6.7, 3.6, 1H),
9
J. AM. CHEM. SOC. VOL. 126, NO. 36, 2004 11199