1308 Chem. Res. Toxicol., Vol. 14, No. 9, 2001
Kim et al.
module 125 and photodiode array detector module 168. Columns
used were YMC-ODS-AQ (Waters, Milford, MA), 4.6 × 250 mm
or 10 × 250 mm, or Luna C-8 or Phenyl-Hexyl (Phenomenex,
Torrance, CA)), 4.6 × 250 mm or 10 × 250 mm. Centrifugal
vacuum evaporation was performed using a RC10.22 evaporator
equipped with a Titan Trap (J ouan, Winchester, VA).
benzene was evaporated under reduced pressure and the residue
was purified by silica gel chromatography (10 and 20% MeOH/
CH2Cl2 or benzene) to give compound 8 as a yellow powder (300
1
mg, 54% yield); mp 184 °C [lit. (16) mp 202-203 °C] H NMR
(300 MHz, Me2SO-d6,) δ 11.58 (s, 1H, CHO), 9.36-9.32 (m, 1H,
H10), 9.28-9.25 (m, H11), 9.03 (d, 1H, H7, J ) 9.6 Hz), 8.65 (d,
1H, H5, J ) 9.2 Hz), 8.52 (d, 1H, H12, J ) 7.8 Hz), 8.39 (d, 1H,
H1, J ) 7.5 Hz), 8.32 (d, 1H, H3, J ) 9.6 Hz), 8.16 (t, 1H, H2,
J ) 7.5 Hz), 7.97-7.94 (m, 3H, H4, 8, 9).
Sp ectr oscop y. Absorption spectra were obtained on a Hi-
tachi U-3000 spectrophotometer. Fluorescence spectra were
obtained on a PC1 Photon Counting Spectrofluorometer (ISS,
Champaign, IL). Both types of spectra were obtained in phos-
phate buffer (10 mM Na2HPO4/NaH2PO4, 1.0 M NaCl, 50 µM
Na2EDTA, pH 7.0) at ambient temperature. Samples were
prepared at a concentration of 1.6 µM of modified strand
(calculated ꢀ at 260 nm, 12.65 × 104) and 1.7 µM complementary
strand (calculated ꢀ at 260 nm, 7.76 × 104).
6-Am in om et h ylb en zo[a ]p yr en e (10, 6-NH2CH 2BP ). 6-
Formylbenzo[a]pyrene (8, 28 mg, 0.1 mmol) was suspended in
1 mL of anhydrous benzene. Sodium bis(trimethylsilyl)amide
(0.1 mmol) was added dropwise over 3 min; the suspension was
stirred for 20 min at room temperature as the solid went into
solution. Chlorotrimethylsilane (0.1 mmol) was added dropwise
over 2 min and stirring was continued for an additional 20 min.
Silylimine 9 was reduced in situ without isolation. Borane-
tetrahydrofuran complex (1 M solution in THF, 100 µL, 0.1
mmol) was added and the reaction was stirred for 30 min. After
addition of 2 M HCl/MeOH (0.5 mL), the reaction was stirred
at room temperature for 30 min, poured into 10 mL of 0.1 M
NaOH, and extracted 4 times with ethyl acetate. The combined
extracts were dried (Na2SO4) and concentrated in vacuo. The
residual yellow oil was chromatographed on silica gel (40 g)
(eluted with CH2Cl2:MeOH, 90:10) to give 10 (12 mg, 43%) as a
yellow powder which migrated as one spot (with some tailing)
on TLC. TLC Rf ) 0.26, (CH2Cl2:MeOH, 9:1); mp 163-164 °C;
1H NMR (400 MHz, Me2SO-d6) δ 9.28-9.26 (m, 1H, H10), 9.25
(d, 1H, H11, J ) 9.1 Hz), 8.75-8.73 (m, 1H, H7), 8.48 (d, 1H,
H5, J ) 9.6 Hz), 8.41 (d, 1H, H12, J ) 9.2 Hz), 8.34 (dd, 1H,
H1, J 1 ) 7.8, J 2 ) 0.9 Hz), 8.20 (dd, 1H, H3, J 1 ) 7.3, J 2 ) 0.7
Hz), 8.09 (d, 1H, H2, J ) 9.6 Hz), 8.04 (t, 1H, H4, J ) 7.6 Hz),
7.90-7.87 (m, 2H, H8, 9), 4.83 (s, 2H, CH2). HRMS (FAB) [MH+]
calcd for C21H16N: 281.1228, Found: 281.1204.
2′-Deoxy-N6-(b en zo[a ]p yr en -6-ylm et h yl)a d en osin e (6,
N6-6MeBP d Ad o). 6-Chloropurine-2′-deoxyriboside (11) (17, 18)
(6 mg, 0.02 mmol) and compound 10 (3 mg, 0.01 mmol) were
dissolved in 400 µL of anhydrous Me2SO and 19 µL (0.11 mmol)
of N,N-diisopropylethylamine (DIPEA) was added to the solu-
tion. The mixture was stirred for 4 h at 55 °C. The product was
purified directly from the reaction mixture by HPLC (YMC-
ODS-AQ column, 10 × 250 mm) with the following gradient:
(A) H2O, (B) CH3CN, 10% to 20% B over 5 min, hold for 3 min,
20% to 99% B over 10 min, hold for 5 min; flow rate 4 mL/min.
Adduct 6 eluted at 20.8 min. The adduct was recovered almost
quantitatively (98%). 1H NMR (400 MHz, Me2SO-d6,) δ 9.28 (d,
2H, H10, H11, J ) 9.0 Hz), 8.77 (d, 1H, H7, J ) 8.4 Hz), 8.63
(d, 1H, H5, J ) 9.4 Hz), 8.45 (d, 1H, H12, J ) 9.1 Hz), 8.36 (d,
1H, H1, J ) 7.7 Hz), 8.30 (s, br, 1H, H2 adenine), 8.21 (d, 1H,
H3, J ) 7.3 Hz), 8.08 (t, 1H, H2, J 1 ) 9.3, J 2 ) 7.2 Hz), 8.05 (s,
1H, H8 adenine), 8.04 (d, 1H, H4, J ) 7.6 Hz), 7.86 (m, 2H,
H8,9), 6.36 (t, 1H, H1′), 5.88 (br, 2H, CH2), 5.31 (d, 1H, OH, J
) 4.0 Hz), 5.20 (br, 1H, OH), 4.39 (br, 1H, H3′), 3.87 (d, 1H,
H4′, J ) 2.5 Hz), 3.59-3.50 (m, 2H, H5′, H5′′), 2.72 (m, 1H,
H2′′), 2.27 (m, 1H, H2′). HRMS (FAB) [MH+] calcd for
C31H26N5O3: 516.2036. Found: 516.2045.
1H NMR and 2D spectra were recorded on a Bruker AC 300
or AM 400 NMR spectrometer with Me2SO-d6, CD3CN, CDCl3,
or MeOH-d4 as solvent. COSY spectra were obtained in the
magnitude mode.
Ma ss Sp ectr om etr y. Low and high-resolution FAB mass
spectra were obtained at the Mass Spectrometry Facility at the
University of Notre Dame, Notre Dame, Indiana. Mass spectra
of oligonucleotides were obtained using a Voyager Elite DE
instrument (PerSeptive Biosystems). The system was operated
in the negative ion mode using a matrix mixture of 2′,4′,6′-
trihydroxyacetophenone monohydrate and ammonium hydrogen
citrate.
Oligon u cleotid es. Oligodeoxynucleotides were synthesized
on an Expedite 8909 DNA Synthesizer (PerSeptives Biosystems)
on a 1-µmol scale using either the manufacturer’s standard
phosphoramidites or tert-butylphenoxyacetyl-protected (tBPA)
phosphoramidites and standard synthesis protocol.
CGE. Capillary gel electrophoresis was performed on a
Beckman P/ACE 5500 instrument using the manufacturer’s
ssDNA 100 gel capillary and Tris-borate-urea buffer. Samples
were applied at -10 kV and run at -10 kV at 30 °C.
En zym e Digestion s. The oligonucleotides (0.2-0.6 A260
units), lyophilized in 1.5 mL microfuge tubes, were digested in
a two-stage process. In the first step, buffer (20 µL, 0.01 M Tris-
HCl, 0.01 M MgCl2, pH 7.0) was added, followed by nuclease
P1 (Sigma N-8630, 4 µL). After digesting for 3-6 h at 36 °C,
Tris-HCl buffer (20 µL, 0.1 M, pH 9.0) was added, followed by
snake venom phosphodiesterase (Sigma 5785, 0.04 units) and
alkaline phosphatase (Sigma P-4282, 0.4 units). Digestion was
continued at 37 °C for 3-6 h. H2O-MeOH (1:1, 100 µL) was
added to each sample and the digest was filtered (Ultrafree-
MC, 0.45 µm, centrifugal filters, Millipore). The filters were
rinsed with Me2SO (50 µL) to elute adducted nucleosides 5 and
6 which are not very soluble in water. The digests were analyzed
by HPLC on either a YMC-ODS-AQ or LUNA C-8 column (4.6
× 250 mm), with the following gradient: (A) 0.1 M ammonium
formate, pH 6.4 (B), CH3CN; 1 to 10% B over 15 min; 10 to 99%
B over 20 min, at a flow rate of 1.5 or 1.0 mL/min.
Meltin g Stu d ies. Adducted oligonucleotide and its comple-
ment were dissolved in melting buffer (10 mM Na2HPO4/
NaH2PO4, 1.0 M NaCl, 50 µM Na2EDTA, pH 7.0). The sample
vials were heated to 100 °C, maintained at that temperature
for 3 min, allowed to cool to room temperature and stored in
the refrigerator overnight. Melting studies were performed using
a Varian Cary 04E UV spectrophotometer. UV measurements
were taken at one minute intervals with a 1 °C/min temperature
gradient. The temperature was raised from 10 to 90 °C and
cooled until a plateau was reached and no further hypo-
chromicity was observed at the detection wavelength of 260 nm.
6-F or m ylben zo[a ]p yr en e (8). A mixture of benzo[a]pyrene
(0.50 g, 2 mmol), POCl3 (330 µL, 3.6 mmol), N-methylformanilide
(494 µL, 4.0 mmol), and 5 mL of o-dichlorobenzene was stirred
in an oil bath at 95-100 °C for 2 h (4). The cooled reaction
mixture was poured slowly into an aqueous solution (5 mL)
containing 2.5 g of sodium acetate. The heterogeneous mixture
was filtered. The filtrate was evaporated to dryness and the
residue was dissolved in hot benzene (100 mL) and filtered. The
2′-Deoxy-N2-(ben zo[a ]p yr en -6-ylm et h yl)gu a n osin e (5,
N2-6-MeBP d Gu o). 2-Fluoro-(O6-trimethylsilylethyl)-2′-deoxy-
inosine (12) (19) (10 mg, 0.03 mmol) and 10 (3 mg, 0.01 mmol)
were dissolved in 600 µL of anhydrous Me2SO followed by the
addition of 19 µL (0.11 mmol) of DIPEA. The reaction mixture
was stirred for 5 h at 45 °C. The products were separated
directly from the reaction mixture by HPLC (YMC-ODS-AQ
column, 10 × 250 mm) with the following gradient: (A) H2O,
(B) CH3CN, 50 to 99% B over 10 min, hold for 5 min, 99 to 40%
B over 5 min; 40 to 50% B over 5 min; flow rate of 4.0 mL/min.
Products eluted at 6.4 min (compound 5) and 17.2 min (13, O6-
trimethylsilylethyl-protected 5). Compound 5 (0.6 mg, 10%) and
compound 13 (1.9 mg, 27%) were collected. Adduct 13 (1.9 mg)
was dissolved in 1 mL of H2O-MeOH (1:2). Hydrochloric acid
(0.05 M, 80 µL) was added and the mixture was stirred for 5 h
at room temperature and 3 h at 50 °C to ensure complete