Formation of a Base Triplets
J . Org. Chem., Vol. 65, No. 22, 2000 7469
92% yield) as a white solid slightly contaminated by trace
amounts of 5 and N,N-diisopropylethylamine. This material
was sufficiently pure for the next transformation.
Characterization of crude 4: Rf ) 0.33 (CH2Cl2/CH3OH 9:1);
1H NMR (CDCl3) δ ) 7.88 (s, 2H), 7.83 (d, 2H, J ) 6.8 Hz),
7.68 (d, 2H, J ) 6.4 Hz), 7.44 (t, 2H, J ) 7.2 Hz), 7.38-7.32
(m, 4H), 5.61 (sb, 3H), 5.34 (d, 1H, J ) 3.2 Hz), 4.64-4.62 (m,
1H), 4.07-4.05 (m, 1H), 3.90-3.82 (m, 2H) ppm.
strand a pyrimidine is preferred in the third strand on
the basis of minimized steric contacts.2,28 A dC residue
tethering a naphthalene diimide intercalator has been
shown to be selective for dC-dG base pair targets.29
Although a target dC residue offers only a single
Hoogsteen hydrogen bonding site (the N4-amino group),
it appeared that a dC residue in the third strand could
be positioned to form a base triplet essentially isomorphic
with dT-dA-dT or dC+-dG-dC. In this orientation, its N3-
nitrogen could function as a hydrogen bond acceptor. Its
effectiveness in this role will depend in part upon its pKa
value. Steric constraints, possibly involving the O2-
carbonyl might reduce the stability of the simple C-C-G
base triplet, consistent with reported observations.1-6,10-16
We therefore decided to examine the use of related
analogue nucleosides, those lacking the O2-carbonyl, as
possible triplex forming residues for C-G target base
pairs. We report here on the synthesis of a new pyrimi-
dine C-nucleosides and triplex forming abilities of this
derivative and a related pyridine C-nucleoside that
exhibit widely varying pKa values.
To a solution of compound 4 (4.1 g, 9.2 mmol) in THF (15
mL) at 0 °C was added acetic acid (2.5 mL, 46 mmol) followed
by 11 mL of a 1 M solution of tetra-n-butylammonium fluoride
in THF. The desilylation reaction was completed in 1 h, based
on TLC analysis. The volatiles were removed in vacuo, and
the residue was separated by flash chromatography on silica
gel using a solvent gradient (CH2Cl2/CH3OH from 30:1 to 1:1)
to yield compound 5 slightly contaminated by N,N-diisopro-
pylethylamine. Crystallization from dichloromethane/methanol
(∼500/1) gave crystals of 5 (1.54 g, yield over two steps 74%).
Characterization of 5: Rf ) 0.47 (CH2Cl2/CH3OH 4:1); UV-
vis λmax (CH3OH) 232 (ꢀ ) 19900 l/Mcm), 301 (ꢀ ) 2880 l/Mcm)
nm; IR (KBr) 3393 (s), 3208 (sb), 3024 (m), 2967 (m), 2934
(m), 2890 (m), 2839 (m), 1754 (s), 1647 (s), 1608 (s), 1558 (s),
1
1496 (s) cm-1; H NMR (D2O) δ 8.28 (s, 2H), 5.10 (dd, 1H, J 1
) 5.6 Hz, J 2 ) 19.8 Hz), 4.05 (t, 1H, J ) 2.8 Hz), 3.74 (dd, 1H,
J 1 ) 2.8 Hz, J 2 ) 18.4 Hz), 3.71 (dd, 1H, J 1 ) 2.8 Hz, J 2
)
18.4 Hz), 2.81 (dd, 1H, J 1 ) 5.6 Hz, J 2 ) 18.4 Hz), 2.51 (dd,
1H, J 1 ) 10.8 Hz, J 2 ) 18.4 Hz) ppm; 13C NMR (DMSO-d6) δ
214.4, 163.6, 157.2, 121.7, 82.7, 73.2, 60.5, 44.1 ppm; mp 148-
149 °C; HRMS calcd for C9H11N3O3 (M + 1) 210.0879, found
210.0880.
Exp er im en ta l Section
Ma ter ia ls. 1H NMR and 13C NMR used TMS as the internal
standard; 31P NMR used phosphoric acid as the external
standard. Flash chromatography was performed using silica
gel 60 with particle size 35-75 µm (EM Science, Germany).
Thin-layer chromatography was performed on Silica Gel 60
F254 precoated TLC aluminum sheet (EM Science, Germany).
Visualization by UV (254 nm) lamp and/or by treating with a
solution of 10% sulfuric acid, followed by heating. All reactions
were carried out under nitrogen, using purified and distilled
solvents. Pyridine, acetonitrile and THF were dried with CaH2
and distilled. Other dry solvents were purchased from Aldrich
Chemical Co and used without further purification. The four
common 2′-deoxynucleotide phosphoramidites and 3′ terminal
nucleoside-bound controlled pore glass (CPG) supports were
purchased from Glen Research (Sterling, VA).
2-Am in o-5-(2-d eoxy-â-D-r ibofu r a n osyl)p yr im id in e (6).
To a solution of compound 5 (1.4 g, 6.7 mmol) in acetonitrile
(50 mL) and acetic acid (60 mL) at 0 °C was added sodium
triacetoxyborohydride (4 g, 18.9 mmol). The reaction was
complete within 1 h, realized by TLC analysis. Volatiles were
removed in vacuo. Sodium carbonate (3 g) was added into the
solution of residue in methanol/dichloromethane (1:1, 20 mL).
The mixture was stirred at ambient temperature for 1 h, and
then the solvent was removed in vacuo. The solid residue was
isolated with flash chromatography on silica gel (CH2Cl2/
CH3OH from 10:1 to 4:1) to give compound 6 (1.3 g, yield 90%).
Compound 6 was recrystallized from mixing solvent (CH3OH/
CH2Cl2 1:400): Rf ) 0.28 (CH2Cl2/CH3OH 4:1); UV-vis λmax
(CH3OH) 230 (ꢀ ) 32600 l/Mcm), 297 (ꢀ ) 5470 l/Mcm) nm; IR
(KBr) 3354 (s), 3169 (s), 3024 (s), 2979 (w), 2957 (w), 2929 (w),
Meth od s. 2-Am in o-5-iod op yr im id in e (2). To a solution
of 2-aminopyrimidine (1) (19 g, 0.20 mol) in acetic acid (200
mL), sulfuric acid (2.5 mL), and water (30 mL) were added
iodine (21.7 g, 0.086 mol) and periodic acid dihydrate (6.5 g,
0.029 mol). The mixture was stirred at 90 °C for 24 h and
poured into 10% Na2S2O3 aqueous solution to remove unre-
acted iodine, and then it was extracted with methylene
chloride. Removing methylene chloride gave solid crude com-
pound. Recrystallization from water gave pure compound 2
(39 g, 90% yield): Rf ) 0.26 (CH2Cl2/CH3OH 95/5) UV-vis
2912 (w), 2901 (w), 2856 (w), 1659 (s), 1569 (m), 1508 (s) cm-1
;
1H NMR (CD3OD) δ 8.30 (s, 1H), 4.98 (dd, 1H, J 1 ) 5.2 Hz, J 2
) 10.4 Hz), 4.34-4.33 (m, 1H), 3.91-3.88 (m, 1H), 3.66 (dd,
1H, J 1 ) 4.4 Hz, J 2 ) 12.4 Hz), 3.63 (dd, 1H, J 1 ) 5.2 Hz, J 2
) 12.4 Hz), 2.14 (ddd, 1H, J 1 ) 1.6 Hz, J 2 ) 5.2 Hz, J 3 ) 13.2
Hz), 1.99 (ddd, 1H, J 1 ) 6.0 Hz, J 2 ) 10.4 Hz, J 3 ) 13.2 Hz)
ppm; 13C NMR (CD3OD) δ 167.95, 161.85, 128.53, 92.81, 81.16,
78.00, 67.47, 47.59 ppm; mp 138-139 °C; HRMS calcd for
C9H13N3O3 (M + 1) 212.1035, found 212.1036.
λ
max(CH3OH) 241 (ꢀ ) 26950 l/Mcm), 317 (ꢀ ) 3090 l/Mcm)
nm; IR (KBr) 3320 (sb), 3180 (s), 1636 (s), 1569 (s), 1541 (s),
1491 (s), 797 (s), 568 (sb), 517 (s), 478 (s) cm-1 1H NMR
;
2-[N-[1-(Dim eth ylam in o)eth ylidin e]am in o]-5-(2′-deoxy-
â-D-r ibofu r a n osyl)p yr im id in e (7). To a solution of com-
pound 6 (1.06 g, 5 mmol) in methanol (200 mL) was added
N,N-dimethylacetamide dimethyl acetal (2.0 g, 15 mmol), and
the reaction mixture was stirred at 78 °C for 24 h. Volatiles
were removed in vacuo, and the resulting residue was sepa-
rated by column chromatography on silica gel (CH2Cl2/CH3-
OH 20:1) to afford compound 7 (1.3 g, 94% yield), a highly
hygroscopic solid: Rf ) 0.40 (CH2Cl2/CH3OH 4:1); UV-vis λmax
(CH3OH) 206 (ꢀ ) 7490 l/Mcm), 240 (ꢀ ) 6990 l/Mcm), 276 (ꢀ
) 14240 l/Mcm) nm; IR (KBr) 3364 (sb), 3011 (w), 2923 (s),
2873 (m), 1620 (s), 1590 (s), 1532 (s), 1400 (s), 1104 (s), 1060
(s), 1023 (s), 947 (m), 866 (m), 828 (m) cm-1; 1H NMR (CDCl3)
δ 8.50 (s, 2H), 5.08 (dd, 1H, J 1 ) 5.6 Hz, J 2 ) 10.0 Hz), 4.46-
4.44 (m, 1H), 4.03 (sb, 2H), 4.01-3.97 (m, 1H), 3.72 (dd, 1H,
J 1 ) 4.4 Hz, J 2 ) 11.6 Hz), 3.68 (dd, 1H, J 1 ) 4.8 Hz, J 211.6
Hz), 3.08 (s, 6H), 2.25 (ddd, 1H, J 1 ) 2.0 Hz, J 2 ) 5.6 Hz, J 3
) 12.8 Hz), 2.06 (s, 3H), 1.99 (ddd, 1H, J 1 ) 6.0 Hz, J 2 ) 10.0
Hz, J 3 ) 12.8 Hz) ppm; 13C NMR (CDCl3) δ 166.44, 161.32,
156.62, 126.67, 87.77, 76.09, 73.12, 62.94, 43.09, 38.40, 16.81
ppm; HRMS calcd for C13H21N4O3 281.1614, found 281.1616.
(CDCl3) δ 8.41 (s, 2H), 5.06 (sb, 2H) ppm; 13C NMR (CDCl3) δ
162.3, 161.5, 75.9 ppm; mp 179-180 °C; HRMS calcd for C4H4-
IN3 (M + 1) 221.9528, found 221.9527.
5-(â-D-Glycer op en tofu r a n -3′-u los-1′-yl)-2-a m in op yr im i-
d in e (5). A mixture of bis(dibenzylideneacetone)palladium
(288 mg, 0.5 mmol) and tris(pentaflorophenyl)phosphine (532
mg, 1.0 mmol) in acetonitrile (250 mL) was stirred under
nitrogen at room temperature for 1 h. N,N-Diisopropylethyl-
amine (8 mL, 45 mmol), 1,4-anhydro-2-deoxy-3-O-[(1,1-di-
methylethyl)diphenylsilyl]-D-erythro-1-enitol (3)1 (3.55 g, 10
mmol), and 2 (2.22 g, 10 mmol) were then added, and the
mixture was refluxed under nitrogen for 66 h. After the
volatiles were removed in vacuo, the residue was purified by
flash chromatography on silica gel using a solvent gradient
(CH2Cl2/CH3OH from 27:1 to 10:1) to give compound 4 (4.1 g,
(28) Vanvlijmen, H. W. T.; Rame, G. L.; Pettitt, B. M. Biopolymers
1990, 30, 517-532.
(29) Gianolio, D. A.; McLaughlin, L. W. J . Am. Chem. Soc. 1999,
121, 6334-6335.