1666 J . Org. Chem., Vol. 63, No. 5, 1998
Ueno et al.
and the residue was partitioned between MeCN and hexane.
The MeCN layer was evaporated under reduced pressure, and
the residue was dissolved in MeOH/THF (1:1, 40 mL). Aque-
ous H2O2 (30%, 1.3 mL, 38 mmol), KF (1.05 g, 18.1 mmol),
and KHCO3 (400 mg, 4.00 mmol) were added to the above
solution, and the resulting mixture was stirred at room
temperature for 16 h. Aqueous Na2S2O3 solution (1 M, 60 mL)
was added, and the resulting insoluble materials were filtered
off. The filtrate was evaporated under reduced pressure, and
the residue was purified by column chromatography (SiO2,
1-3% MeOH in CHCl3) to give 6 (2.05 g, 87%) as a white
foam: 1H NMR (500 MHz, CDCl3) δ 8.97 (br s, 1H), 7.62 (s,
1H), 7.40-6.83 (m, 13H), 6.48 (t, 1H, J ) 7.2), 4.53 (m, 1H),
3.85 (m, 1H), 3.79 (s, 6H), 3.58 (ddd, 1H, J ) 10.3, 6.7, 3.5),
3.31 (d, 1H, J ) 9.9), 3.24 (d, 1H, J ) 9.9), 2.46-2.43 (m, 2H),
2.05 (ddd, 1H, J ) 15.0, 8.2, 3.5), 1.81 (ddd, 1H, J ) 15.0, 6.7,
3.3), 1.38 (s, 3H); FABMS m/z 589 [M+ + 1]; HRFABMS calcd
for C33H37N2O8 589.2549, found 589.2522.
NaHCO3 and brine, dried (Na2SO4), and concentrated. The
residue was purified by column chromatography (a neutralized
SiO2, 50-100% AcOEt in hexane) to give 5 (385 mg, 72%) as
a foam: 31P NMR (202 MHz, CDCl3) δ 150.28, 149.88; FABMS
m/z 971 [M+ + 1]; HRFABMS calcd for C47H59F3N6O11
P
971.3931, found 971.3894.
Syn th esis of ODNs. ODNs were synthesized on a DNA
synthesizer (Applied Biosystem model 381A) by the phos-
phoramidite method. The fully protected ODNs were then
deblocked and purified by the same procedure as for the
purification of normal ODNs. That is, each ODN linked to
the resin was treated with concentrated NH4OH at 55 °C for
16 h, and the released ODN protected by a DMTr group at
the 5′-end was chromatographed on a C-18 silica gel column
(1 × 10 cm, Waters) with a linear gradient of MeCN from 0 to
30% in 0.1 M TEAA buffer (pH 7.0). The fractions were
concentrated, the residue was treated with aqueous 80% AcOH
at room temperature for 20 min and then the solution was
concentrated and the residue was coevaporated with H2O. The
residue was dissolved in H2O and the solution was washed
with Et2O, and then the H2O layer was concentrated to give
deprotected ODN 16 (95), 17 (65), 18 (48), 19 (38), 20 (64), 22
(32), 23 (61), and 24 (33). The yields are indicated in
parentheses as OD units at 260 nm on a 1 µmol scale.
Electr osp r a y Ion iza tion Ma ss Sp ectr om etr y. Spectra
were obtained on a Quattro II (Micromass, Manchester, U.K.)
triple quadrupole mass spectrometer equipped with an ESI
source in the negative-ion mode. The HPLC-purified ODN
samples were dissolved in aqueous 50% 2-propanol containing
1% triethylamine (10 pmol ODN/µL) and introduced into the
ion source through a loop injector with a carrier solvent, 33%
aqueous MeOH, flowing at 10 mL/min flow rate. About 15
scans were acquired over approximately 1 min and combined
to obtain smoothed spectra. All molecular masses of the ODNs
were calculated from the multiple-charge negative-ion spectra.
The observed average molecular masses of 16 and 22 were
5860.9 and 5187.5, respectively, and fit the calculated molec-
ular weights (theoretical average molecular masses) for these
compounds, i.e., 5860.9 (for 16, C188H245N65O118P18) and 5187.5
(for 22, C167H220N56O105P16) within a commonly accepted error
range of ESI MS, 0.01%.
5′-O-(Dim e t h oxyt r it yl)-4′-C-(1-h yd r oxye t h yl)t h ym i-
d in e (13). A solution of 7 (313 mg, 0.400 mmol), Bu3SnH (320
µL, 1.19 mmol), and AIBN (20 mg, 0.12 mmol) in benzene (4
mL) was stirred at 60 °C for 4 h. The solvent was evaporated
under reduced pressure, and the residue was partitioned
between MeCN and hexane. The MeCN layer was evaporated
under reduced pressure. The residue was treated under
Tamao oxidation conditions as described above for 6 to give
13 (177 mg, 75%) as a white foam: 1H NMR (270 MHz, CDCl3)
δ 8.30 (br s, 1/3H), 8.23 (br s, 2/3H), 7.41-6.85 (m, 14H), 6.51
(t, 1/3H, J ) 7.1), 6.44 (dd, 2/3H, J ) 5.9, 8.7), 4.84 (m, 1/3H),
4.74 (m, 2/3H), 4.18-4.09 (m, 1H), 3.81 (s, 6H), 3.58 (d, 2/3H),
3.50 (d, 2/3H, J ) 10.0), 3.29 (d, 2/3H, J ) 10.0), 3.21 (s, 2/3H),
2.90 (d, 2/3H), 2.71 (d, 1/3H), 2.49-2.36 (m, 2H), 1.54 (s, 2H),
1.46 (s, 1H), 1.15-1.11 (m, 3H); FABMS m/z 588 [M+];
HRFABMS calcd for C33H36N2O8 588.2469, found 588.2488.
5′-O-(Dim e t h oxyt r it yl)-4′-C-[2-[[N -[2-[N -(t r iflu or o-
a cetyl)a m in o]eth yl]ca r ba m oyl]oxy]eth yl]th ym id in e (14).
N,N′-Carbonyldiimidazole (80 mg, 0.5 mmol) and DMAP (40
mg, 0.3 mmol) were added to a solution of 6 (966 mg, 1.6 mmol)
in DMF (80 mL), and the mixture was stirred at room
temperature. After 2, 4, and 6 h, further amounts of N,N′-
carbonyldiimidazole (80 mg, 0.5 mmol) were added to the
mixture. After 15 h, 1,2-diaminoethane (0.55 mL, 8.2 mmol)
was added to the mixture, which was stirred at room temper-
ature. After 3 h, the solvent was removed by evaporation. The
residue was diluted with CHCl3. The organic layer was
washed with aqueous 0.1 M NaH2PO4, dried (Na2SO4), and
evaporated under reduced pressure. The residue was dissolved
in MeOH (80 mL). Ethyl trifluoroacetate (976 µL, 8.2 mmol)
and Et3N (1.1 mL, 8.2 mmol) were added to the solution with
stirring at room temperature. After 14 h, the solvent was
removed by evaporation. The residue was diluted with CHCl3.
The organic layer was washed with H2O and brine, dried (Na2-
SO4), and evaporated under reduced pressure. The residue
was purified by column chromatography (SiO2, 1-10% EtOH
in CHCl3) to give 14 (818 mg, 65%) as a white foam: 1H NMR
(270 MHz, CDCl3) δ 8.92 (br s, 1H), 7.80 (br t, 1H), 7.42-6.84
(m, 14H), 6.42 (t, 1H, J ) 6.9), 5.37 (br t, 1H), 4.49 (m, 1H),
4.20 (m, 1H), 4.07 (m, 1H), 3.81 (s, 6H), 3.45 (m, 2H), 3.35 (m,
2H), 3.29-3.28 (m, 2H), 2.98 (d, 1H, J ) 5.4), 2.42-2.37 (m,
2H), 2.14-1.92 (m, 2H), 1.57 (s, 3H); FABMS m/z 771 [M++1];
HRFABMS calcd for C38H42N4O10F3 771.2850, found 771.2841.
5′-O-(Dim e t h oxyt r it yl)-4′-C-[2-[[N -[2-[N -(t r iflu or o-
a cetyl)a m in o]eth yl]ca r ba m oyl]oxy]eth yl]th ym id in e 3′-
O-(2-Cya n oeth yl N,N-d iisop r op ylp h osp h or a m id ite) (5).
After successive coevaporation with pyridine, 14 (423 mg, 0.55
mmol) was dissolved in CH2Cl2 (10 mL) containing N,N-
diisopropylethylamine (0.192 mL, 1.1 mmol). Chloro(2-cya-
noethoxy)(N,N-diisopropylamino)phosphine (0.184 mL, 0.83
mmol) was added to the solution, and the reaction mixture
was stirred for 20 min at room temperature. After 30 min,
further amounts of N,N-diisopropylethylamine (48 µL) and
chloro(2-cyanoethoxy)(N,N-diisopropylamino)phosphine (61 µL)
were added to the mixture. After 1.5 h, aqueous saturated
NaHCO3 and CHCl3 were added to the mixture, and the
separated organic layer was washed with aqueous saturated
Th er m a l Den a t u r a t ion a n d CD Sp ect r oscop y. Each
solution contains ODN (3 µM) and the complementary DNA
25 (3 µM) or RNA 26 (3 µM) in an appropriate buffer. The
solution containing each ODN was heated at 90 °C for 10 min
and then cooled gradually to an appropriate temperature and
used for the thermal denaturation studies. Thermal-induced
transitions of each mixture were monitored at 260 nm on a
Perkin-Elmer Lambda2S. Sample temperature was increased
0.5 °C/min. Samples for CD spectroscopy were prepared by
the same procedure used in the thermal denaturation study,
and spectra were measured on a J ASCO J 720 spectropola-
rimeter at 15 °C. The ellipticities of duplexes were recorded
from 200 to 320 nm in a cuvette with a path length 1 mm. CD
data were converted into mdeg‚mol of residues-1‚cm-1
.
P a r tia l Hyd r olysis of ODN w ith Sn a k e Ven om P h os-
p h od iester a se. Each ODN labeled with 32P at the 5′-end (10
pmol) was incubated with snake venom phosphodiesterase (0.4
µg) in the presence of Torula RNA (0.26 OD units at 260 nm)
in a buffer containing 37.5 mM Tris-HCl (pH 8.0) and 7.5 mM
MgCl2 (total 20 µL) at 37 °C. At appropriate periods, aliquots
of the reaction mixture were separated and added to a solution
of EDTA (5mM, 10 µL), and then the mixture were heated for
3 min at 90 °C. The solutions were analyzed by electrophoresis
on 20% polyacrylamide gel containing 7 M urea.
P a r tia l Hyd r olysis of ODN w ith DNa se I. Each ODN
labeled with 32P at the 5′-end (10 pmol) was incubated with
DNase I (1 unit) in the presence of Torula RNA (0.26 OD units
at 260 nm) in a buffer containing 100 mM sodium acetate (pH
6.0) and 5 mM MgCl2 (total 20 µL) at 37 °C. At appropriate
periods, aliquots of the reaction mixture were separated and
added to a solution of EDTA (5mM, 10 µL), and then the
mixtures were heated for 3 min at 90 °C. The solutions were
analyzed by gel electrophoresis as described above.