Z. Huang et al.
COMMUNICATION
1H, NH2), 6.86–7.48 (m, 13H, arom. H), 8.30 ppm (s, 1H, H-6).
compensating the duplex destabilization by the disruption of
the 5-CH3/p interaction. The collected diffraction data,
phasing, and refinement statistics of the Se-DNA structure
(3IJN) are included in the Supporting Information (Ta-
bles S1 and S2).
13C NMR (100 MHz, DMSO-d6): d=ꢁ4.86 and ꢁ4.69 [Si
ACHTUGNTRNEN(UNG CH3)2], 7.31
(SeCH3), 17.96 [SiCACHTUNTRGENNUG(CH3)], 25.74 [SiCACHTUGNTERN(NUNG CH3)], 41.74 (C-2’), 55.26 (OMe),
62.88 (C-5’), 72.23 (C-3’), 85.55 (C-4’), 87.05 (arom. C), 87.16 (C-1’),
103.45 (C-5), 113.23 (arom. C), 126.94 (arom. C), 128.15 (arom. C),
130.11 (arom. C), 135.50 (arom. C), 141.74 (C-6), 144.41 (arom. C),
149.89 (C-2), 155.46 (arom. C), 158.66 (C-4), 161.46 (arom. C),
165.55 ppm (arom. C). HR-MS (ESI-TOF, possitive ion mode): calcd for
C37H47N3O6SeSi [M+H]+: 738.2478, found 738.2468.
Conclusions
4-N-Benzoyl-5-methylseleno-3’-tert-butyldimethylsilyl-5’-O-(4,4-
dimethoxytrityl)-2’-deoxycytidine (3)
In summary, we have successfully synthesized the novel SeC-
phosphoramidite and incorporated the nucleoside into DNA
for biophysical and structural studies. Our experimental re-
sults indicate that the Se functionality at the C-5 position of
cytidine does not perturb the DNA duplex structure; the
thermostability and structure of Se-DNA in its duplex form
is highly similar to the corresponding native DNA. We
expext that our study on 5-methylcytosine with the selenium
modification will encourage further investigation on m5C, its
epigenetic mechanism, and methyltransferase inhibitor
design. Furthermore, the synthesis reported herein offers a
useful derivatization strategy for nucleic acid X-ray crystal-
lography.
5-Methylseleno-3’-tert-butyldimethylsilyl-5’-O-(4,4-dimethoxytrityl)-2’-de-
oxycytidine (300 mg, MW 751.3, 0.4 mmol) was placed in a flask and
dried under high vacuum for 1 h before anhydrous pyridine (10 mL) was
added. Subsequently, benzoyl chloride (0.03 mL, 0.6 mmol, 1.5 equiv) was
added dropwise, and the reaction mixture was stirred for 1 h at room
temperature. After the reaction was completed (monitored by TLC, 30%
ethyl acetate in n-hexane, Rf =0.5), the crude product was extracted with
brine and EtOAc. The organic phase was removed and the aqueous
phase was extracted thrice with EtOAc. The combined organic phase was
dried over anhydrous MgSO4, filtered, and the organic solvents were
evaporated under reduced pressure. The residue was purified by column
chromatography on silica gel (10–50% EtOAc in n-hexane) to afford 3
as
a
yellow–green solid (287 mg, 84% yield). 1H NMR (400 MHz,
(CH3)2], 0.86 (s, 9H, tert-butyl),
DMSO-d6): d=0.09 and 0.04 [2x s, 6H, SiAHCUTNGTRENNUNG
2.02 (s, 3H, SeCH3), 2.18–2.20 and 2.43–2.52 (2x m, 2H, H-2’), 3.29–3.33
and 3.43–3.46 (2x m, 2H, H-5’), 3.81 (s, 6H, 2x OMe), 4.05–4.08 (m, 1H,
H-3’), 4.41–4.45 (m, 1H, H-4’), 6.30–6.34 (t, J=6.4 Hz, 1H, H-1’), 6.86–
7.56 (m, 18H, arom. H), 7.88 (s, 1H, NH), 8.32 ppm (s, 1H, H-6).
Experimental Section
13C NMR (100 MHz, DMSO-d6): d=ꢁ4.89 and ꢁ4.69 [Si
ACHTUGNTRNEN(UNG CH3)2], 1.03
(SeCH3), 17.95 [SiCACHTUNTRGENNUG(CH3)], 25.73 [SiCACHTUGNTERN(NUNG CH3)], 41.86 (C-2’), 55.26 (OMe),
Materials
63.05 (C-5’), 72.41 (C-3’), 86.30 (C-4’), 86.77 (C-5), 87.24 (C-1’), 113.27
(arom. C), 127.07 (arom. C), 128.13 (arom. C), 128.27 (arom. C), 129.38
(arom. C), 130.09 (arom. C), 132.67 (arom. C), 133.68 (C-6), 135.51
(NHCO), 144.41 (arom. C), 144.36 (C-2), 158.69 ppm (C-4). HR-MS
(ESI-TOF, negative ion mode): calcd for C44H51N3O7SeSi [MꢁH]ꢁ:
840.2583, found, 840.2570.
Unless stated otherwise, reagents and chemicals were purchased from
Sigma, Fluka, or Aldrich. Phosphoramidites used in the solid-phase syn-
thesis of oligonucleotides were obtained from Glen Research. THF, di-
chloromethane, and acetonitrile were distilled under argon. Solid starting
materials were dried under high vacuum before use. All reactions were
performed under argon. Thin layer chromatography (TLC) was per-
formed on analytical Merck 60 F254 plates (0.25 mm thickness) and vi-
sualized under UV light. Flash column chromatography was performed
using Fluka silica gel 60 (mesh size 0.040–0.063 mm) with a silica gel/
crude compound weight ratio of approximately 30:1. 1H and 13C NMR
spectra were recorded on a Bruker-400 (400 MHz) spectrometer. Chemi-
cal shifts are reported in ppm relative to tetramethylsilane and coupling
constants are in Hz. High-resolution mass spectra were recorded at Geor-
gia State University.
4-N-Benzoyl-5-methylseleno-5’-O-(4,4-dimethoxytrityl)-2’-deoxycytidine
(4)
4-N-Benzoyl-5-methylseleno-3’-tert-butyldimethylsilyl-5’-O-(4,4-dime-
thoxytrityl)-2’-deoxycytidine (3, 280 mg, MW 855.3, 0.33 mmol) was
placed in a flask, dried under high vacuum, and dissolved in anhydrous
THF (3 mL). The solution was placed in an ice–water bath under dry
argon. Next, tetrabutylammonium fluoride (0.44 mL of a 1m solution in
THF, 1.2 equiv) and acetic acid (0.03 mL, 1.2 equiv) were injected drop-
wise simultaneously to maintain the pH value at 7. After stirring over-
night, the reaction was completed (monitored by TLC, 3% MeOH in
CH2Cl2, Rf =0.35). The crude product was extracted with EtOAc and
brine (3x), and the combined organic layer was dried over anhydrous
MgSO4, filtered, and concentrated. The residue was purified by column
chromatography on silica gel (5% MeOH in CH2Cl2) to afford 4 as a
white solid (225 mg, 91% yield). 1H NMR (400 MHz, DMSO-d6): d=
2.04 (s, 3H, SeCH3), 2.21–2.26 and 2.69–2.76 (2x m, 2H, H-2’), 3.34–3.47
(2x m, 2H, H-5’), 3.79 (s, 6H, 2x OMe), 4.15–4.17 (m, 1H, H-3’), 4.46–
4.48 (m, 1H, H-4’), 6.14–6.17 (t, J=6.4 Hz, 1H, H-1’), 6.84–7.79 (m, 18H,
arom-H), 8.48 ppm (s, 1H, H-6). 13C NMR (100 MHz, DMSO-d6): d=
11.02 (SeCH3), 41.99 (C-2’), 55.27 (OMe), 63.11 (C-5’), 72.41 (C-3’), 86.67
(C-4’), 86.94 (arom. C), 87.87 (C-1’), 102.39 (C-5), 113.31 (arom-C),
127.07 (arom. C), 128.04 (arom. C), 128.07 (arom. C), 128.29 (arom. C),
129.68 (arom. C), 129.45 (arom. C), 130.00 (arom. C), 130.92 (arom. C),
132.70 (arom. C), 134.22 (arom. C), 135.47 (NHCO), 144.41 (arom. C),
144.32 (C-2), 150.83 (C-6), 158.69 (C-4), 172.28 ppm (arom. C). HR-MS
(ESI-TOF, possitive ion mode): calcd for C38H38N3O7Se: [M+H]+:
728.1797, found, 728.1898.
5-Methylseleno-3’-tert-butyldimethylsilyl-5’-O-(4,4-dimethoxytrityl)-2’-
deoxycytidine
Diisopropylethyl amine (0.67 mL, 3.19 mmol, 5 equiv), triisopropylbenze-
nesulfonyl chloride (576 mg, 1.59 mmol, 2.5 equiv), and 4-dimethylamino-
pyridine (96 mg, 0.64 mmol, 1 equiv) were added sequentially to a solu-
tion of 5-methylseleno-3’-tert-butyldimethylsilyl-5’-O-(4,4-dimethoxytri-
tyl)-2’-deoxyuridine[1] (MW 752.2, 480 mg, 0.64 mmol) in 10 mL acetoni-
trile. The reaction mixture was stirred for 16 h and monitored by TLC
(EtOAc/n-hexane, 3:7). After completion, an excess of concentrated am-
monium hydroxide solution was added dropwise, and the reaction was
stirred for 1 h at room temperature. After the reaction was completed
(monitored by TLC, 5% MeOH in CH2Cl2, Rf =0.5), the organic solvent
and ammonium hydroxide were evaporated under reduced pressure. Sub-
sequently, the crude product was purified by column chromatography on
silica gel (1–7% MeOH in CH2Cl2). The fractions containing the product
were combined, evaporated, and dried under high vacuum overnight to
yield a yellow solid (307 mg, 64% yield). 1H NMR (400 MHz, DMSO-
d6): d=0.05 (s, 6H, SiCH3), 0.87 (s, 9H, tert-butyl), 1.95 (s, 3H, SeCH3),
2.18–2.25 and 2.58–2.62 (2x m, 2H, H-2’), 3.30–3.33 and 3.46–3.49 (2x m,
2H, H-5’), 3.84 (s, 6H, 2x OMe), 4.03–4.08 (m, 1H, H-3’), 4.42–4.46 (m,
1H, H-4’), 6.11 (s, 1H, NH2), 6.28–6.31 (t, J=5.6 Hz, 1H, H-1’), 6.50 (s,
478
ꢀ 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Chem. Asian J. 2012, 7, 476 – 479