Design and synthesis of a photocleavable fluorescent nucleotide 3′-O-allyl-dGTP-PC-Bodipy-FL-510 as a reversible terminator for DNA sequencing by synthesis

Article abstract of DOI:10.1021/jo060300k

DNA sequencing by synthesis (SBS) using reversible fluorescent nucleotide terminators is potentially an efficient approach to address the limitations of current DNA sequencing techniques. Here, we report the design and synthesis of a 3′-O-allyl photocleav

Full text of DOI:10.1021/jo060300k

Design and Synthesis of a Photocleavable Fluorescent Nucleotide
3′-O-Allyl-dGTP-PC-Bodipy-FL-510 as a Reversible Terminator for
DNA Sequencing by Synthesis
Qinglin Meng,†,‡,§ Dae Hyun Kim,†,| Xiaopeng Bai,†,‡,§ Lanrong Bi,†,‡
Nicholas J. Turro,‡,§ and Jingyue Ju*,†,‡
Columbia Genome Center, Columbia UniVersity College of Physicians and Surgeons,
New York, New York 10032, and Departments of Chemical Engineering, Chemistry, and
Biomedical Engineering, Columbia UniVersity, New York, New York 10027
ju@genomecenter.columbia.edu
ReceiVed February 14, 2006
DNA sequencing by synthesis (SBS) using reversible fluorescent nucleotide terminators is potentially an
efficient approach to address the limitations of current DNA sequencing techniques. Here, we report the
design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide analogue, 3′-O-allyl-dGTP-
PC-Bodipy-FL-510, as a reversible terminator for SBS. The nucleotide is efficiently incorporated by
DNA polymerase into a growing DNA strand to terminate the polymerase reaction. After that, the
fluorophore is photocleaved quantitatively by irradiation at 355 nm, and the allyl group is rapidly and
efficiently removed by using a Pd-catalyzed reaction under DNA-compatible conditions to regenerate a
free 3′-OH group to reinitiate the polymerase reaction. Two cycles of such steps were successfully
demonstrated to sequence a homopolymeric region of a DNA template, facilitating the development of
SBS as a viable approach for high-throughput DNA sequencing.
Introduction
terminate the polymerase reaction. After that, the fluorophore
can be photocleaved quantitatively by irradiation at 355 nm,
and the allyl group is rapidly and efficiently removed by using
a Pd-catalyzed reaction in water to regenerate a free 3′-OH group
to reinitiate the polymerase reaction.
To the best of our knowledge, using 3′-modified dGTP as a
reversible terminator for SBS has not been reported, partly due
to the difficulty of modifying the 3′-OH of guanosine by a
suitable capping group without protecting the guanine base.
Here, we describe the design and synthesis of a 3′-O-allyl
photocleavable fluorescent 7-deaza-dGTP, 3′-O-allyl-dGTP-PC-
Bodipy-FL-510 (10), with a fluorophore attached to the 7
position of the modified guanine base and its successful
application as a reversible terminator to determine two repeated
nucleotide sequences in SBS. Previously, the Pd-catalyzed
deallylation to regenerate a free 3′-OH of the DNA extension
product was carried out in pure water,2 which can destabilize
DNA sequencing is a fundamental tool for biological research
and medical diagnostics, driving disease gene discovery and
gene function studies. DNA sequencing by synthesis (SBS)
using reversible fluorescent nucleotide terminators1 is a poten-
tially efficient approach to address the limitations of current
DNA sequencing techniques, such as throughput and data
accuracy. We have previously reported the design and synthesis
of a 3′-O-allyl photocleavable (PC) fluorescent nucleotide
analogue, 3′-O-allyl-dUTP-PC-Bodipy-FL-510, as a reversible
terminator for SBS.2 The nucleotide can be efficiently incor-
porated by DNA polymerase into a growing DNA strand to
* To whom correspondence should be addressed. Phone: 212-851-5172.
Fax: 212-851-5215.
† Columbia Genome Center, Columbia University College of Physicians and
Surgeons.
‡ Department of Chemical Engineering, Columbia University.
§ Department of Chemistry, Columbia University.
| Department of Biomedical Engineering, Columbia University.
(1) Ju, J.; Li, Z.; Edwards, J.; Itagaki, Y. U.S. Patent 6,664,079, 2003.
(2) Ruparel, H.; Bi, L.; Li, Z.; Bai, X.; Kim, D. H.; Turro, N. J.; Ju, J.
Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 5932-5937.
10.1021/jo060300k CCC: $33.50 © 2006 American Chemical Society
Published on Web 03/24/2006
3248
J. Org. Chem. 2006, 71, 3248-3252

Design and Synthesis of a PhotocleaVable Fluorescent Nucleotide
SCHEME 1. Synthesis of
3′-O-Allyl-dGTP-PC-Bodipy-FL-510 (10)
SCHEME 2. DNA Polymerase Extension Reaction Using
3′-O-Allyl-dGTP-PC-Bodipy-FL-510 (10) as a Reversible
Terminator
NaOH solution using tetrabutylammonium bromide as phase-
transfer catalyst to give a 92% yield of 6 without N2-allylated
product. Sonogashira cross-coupling reaction of 6 with the
terminal alkyne catalyzed by Pd(0)/Cu(I) formed 7 in 94%
yield.6 Next, a one-pot procedure of demethylation7 and
desilylation of 7 gave a moderate 34% yield of 8. Finally 8
was transformed into the corresponding triphosphate 3′-O-allyl-
dGTP 9 following established procedures.8 Coupling 9 with PC-
Bodipy-FL-510 NHS ester9 yielded the target compound, 3′-
O-allyl-dGTP-PC-Bodipy-FL-510 (10).
the primer-template duplex. We report here the identification
of a new condition for rapid quantitative deallylation in a buffer
solution at pH 8.8, which is commonly used for polymerase
reaction. The successful synthesis of compound 10 as a
reversible terminator to sequence through a homopolymer
sequence and the identification of the new deallylation condition
will facilitate the development of SBS as a viable approach for
de novo DNA sequencing.
Results and Discussion
For 3′-O-allyl-dGTP-PC-Bodipy-FL-510 (10) to act as a
reversible terminator for SBS, it is important to establish that
10 can be used to determine a repeated DNA sequence in a
polymerase reaction. To this end, we performed a polymerase
DNA extension reaction using 10 as a substrate in solution as
shown in Scheme 2. This allows the isolation of the DNA
product at each step for detailed molecular structure character-
ization by using MALDI-TOF mass spectrometry (MS) as
shown in Figure 1.
2-Amino-6-methoxy-9-(â-D-2′-deoxyribofuranosyl)-7-deaza-
purine 1 was chosen as the starting material for the synthesis
of 3′-O-allyl-7-(3-aminoprop-1-ynyl)-7-deaza-dGTP 9 (Scheme
1). Compound 1 was first protected by isobutyryl chloride to
yield 2 quantitatively.3 Compound 2 was iodinated at the
7-position by N-iodosuccinimide (NIS) to produce a single
product 3 in 90% yield, as the 2-acylamino group in the
nucleobase promotes the formation of 7-substituted product.4
Compound 3 was deprotected by methanolic sodium methoxide
to afford 4 in 94% yield. 5′-OH of 4 was protected by tert-
butyldimethylsilyl chloride to produce 5 in 88% yield.5 3′-OH
of 5 was subsequently allylated in CH2Cl2 and 40% aqueous
(6) Hobbs, F. W. J. Org. Chem. 1989, 54, 3420-3422.
(7) Ramasamy, K.; Imarura, N.; Robins, R. K.; Revankar, G. R. J.
Heterocycl. Chem. 1988, 25, 1893-1898.
(8) Lee, S. E.; Sidorov, A.; Gourlain, T.; Mignet, N.; Thorpe, S. J.;
Brazier, J. A.; Dickman, M. J.; Hornby, D. P.; Grasby, J. A.; Williams, D.
M. Nucleic Acids Res. 2001, 29, 1565-1573.
(3) Seela, F.; Driller, H. Nucl. Nucl. 1989, 8, 1-21.
(4) Ramzaeva, N.; Seela, F. Hel. Chim. Acta 1995, 78, 1083-1090.
(5) Ryu, E. K.; Ross, R. J.; Matsushita, T.; MacCoss, M.; Hong, C. I.;
West, C. R. J. Med. Chem. 1982, 25, 1322-1329.
(9) Seo, T. S.; Bai, X.; Kim, D. H.; Meng, Q.; Shi, S.; Ruparel, H.; Li,
Z.; Turro, N. J.; Ju, J. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 5926-
5931.
J. Org. Chem, Vol. 71, No. 8, 2006 3249

Meng et al.
peak corresponding to the photocleavage product 12 appears
as the sole dominant peak at m/z 6552. Figure 1C shows a single
peak at m/z 6512, which corresponds to a deallylated photo-
cleavage product 13. The absence of a peak at m/z 6552 proves
that the deallylation reaction was completed with high efficiency.
The next extension reaction was carried out by using this
deallylated photocleavage product 13 as a primer along with
3′-O-allyl-dGTP-PC-Bodipy-FL-510 (10) to yield an extension
product 14 (Figure 1D). DNA products (15 and 16) from
photocleavage (Figure 1E) and deallylation (Figure 1F), respec-
tively, were obtained in a similar manner as described previ-
ously, thereby completing two entire polymerase extension
cycles to sequence a homopolymeric region of a template using
10 as a reversible terminator.
In summary, we have developed a successful strategy for the
synthesis of a 3′-O-allyl-modified 7-deaza-dGTP bearing a
photocleavable fluorophore at the 7 position. This novel
nucleotide analogue is shown to be an excellent substrate for
9°N DNA polymerase A485L/Y409V and can be incorporated
with high efficiency in a polymerase extension reaction. We
have also demonstrated that complete photocleavage to remove
the fluorophore is achieved in 10 s on these DNA products.
Furthermore, we have shown that deallylation can be swiftly
achieved to near completion under mild reaction conditions in
an aqueous environment by using a palladium catalyst. Finally,
we have established that the deallylated DNA product can be
used as a primer to continue the polymerase reaction and that
extension, photocleavage, and deallylation can be performed
with high efficiency. These results provide further proof of the
feasibility of using the allyl group as a reversible capping moiety
for the 3′-OH of the photocleavable nucleotide analogues for
SBS, validating the approach we had previously proposed.1
Thus, the successful engineering of the building blocks of DNA
with synthetic chemistry will facilitate the development of SBS
for high-throughput DNA sequencing and genotyping.
FIGURE 1. Continuous polymerase extension scheme (left) and
MALDI-TOF MS spectra of the resulting DNA products (right).
A synthetic 100-mer DNA corresponding to a portion of exon
7 of the human p53 gene was used as a template to perform the
extension. The sequence in the template immediately adjacent
to the annealing site of the primer had a repeating sequence of
3′-CC-5′. First, a polymerase extension reaction using 10 as a
terminator along with a primer and the above template was
performed. After the reaction, a small portion of the DNA
extension product was characterized by MALDI-TOF MS. The
rest of the product was irradiated at 355 nm for 10 s to cleave
the fluorophore from the DNA and then analyzed by MALDI-
TOF MS. After photocleavage, the DNA product was added to
a deallylation cocktail [1X Thermopol reaction buffer/Na2PdCl4/
P(PhSO3Na)3] to remove the 3′-allyl group in 30 s to yield
quantitatively deallylated DNA product. The deallylated DNA
product with a free 3′-OH group regenerated was then used as
a primer to incorporate 10 in a subsequent second extension
reaction.
Figure 1 (right panel) shows a sequential mass spectrum at
each step of DNA SBS using 10 as a reversible terminator. As
can be seen from Figure 1A, the MALDI-TOF MS spectrum
consists of a distinct peak at m/z 7048 corresponding to the
single-base DNA extension product 11 with 100% incorporation
efficiency, confirming that the reversible terminator 10 can be
incorporated base-specifically by DNA polymerase into a
growing DNA strand. The small peak at m/z 6552 corresponding
to the photocleavage product is due to the partial cleavage
caused by the nitrogen laser pulse (337 nm) used for ionization
in MALDI-TOF MS. Figure 1B shows the photocleavage result
after 10 s irradiation of the DNA extension product at 355 nm.
The peak at m/z 7048 has completely disappeared, whereas the
Experimental Section
2-(2-Methylpropanoyl)amino-6-methoxy-9-[3′,5′-bis-O-(2-
methylpropanoyl)-â-D-2′-deoxyribofuranosyl]-7-deazapurine (2).
To a stirred suspension of 1 (1.00 g; 3.57 mmol) in anhydrous
pyridine (35 mL) was added slowly isobutyryl chloride (3.40 mL;
32.2 mmol) at 0 °C. The reaction mixture was stirred at 0 °C for
1 h. Methanol (2 mL) was then added, and the reaction mixture
was stirred for another 10 min. Then most solvent was removed
under vacuum. Ethyl acetate (200 mL) and saturated aqueous
NaHCO3 (50 mL) were added to the residue. The organic layer
was separated, washed with saturated aqueous NaHCO3 and NaCl,
respectively, and dried over anhydrous Na2SO4. After evaporation
of the solvent, the residue was purified by flash column chroma-
tography over silica gel using ethyl acetate-hexane (1:3∼2) as the
eluent to afford 2 as white foam (1.75 g; 99% yield): 1H NMR
(400 MHz, CD3OD) δ 7.28 (d, J ) 3.7 Hz, 1H), 6.66 (dd, J ) 5.9,
8.6 Hz, 1H), 6.51 (d, J ) 3.7 Hz, 1H), 5.41 (m, 1H), 4.33-4.36
(m, 2H), 4.22 (m, 1H), 4.08 (s, 3H), 2.83-2.96 (m, 2H), 2.54-
2.70 (m, 2H), 2.48-2.54 (ddd, J ) 2.0, 5.9, 14.2 Hz, 1H), 1.15-
1.23 (m, 18H); 13C NMR (100 MHz, CD3OD) δ 178.2, 177.7, 177.4,
164.2, 153.4, 152.5, 123.4, 103.5, 100.7, 85.2, 83.0, 75.9, 65.0,
54.4, 37.9, 36.6, 35.0, 34.9, 19.9, 19.3-19.4 (four peaks); HRMS
(FAB+) calcd for C24H35O7N4 (M + H+) 491.2506, found
491.2503.
2-(2-Methylpropanoyl)amino-6-methoxy-7-iodo-9-[3′,5′-bis-
O-(2-methylpropanoyl)-â-D-2′-deoxyribofuranosyl]-7-deaza-
purine (3). To a vigorously stirred solution of 2 (1.75 g; 3.57 mmol)
in anhydrous DMF (27 mL) was added 95% N-iodosuccimide (NIS)
3250 J. Org. Chem., Vol. 71, No. 8, 2006

Design and Synthesis of a PhotocleaVable Fluorescent Nucleotide
(866 mg; 3.66 mmol). The reaction mixture was stirred at room
temperature for 22 h, and then most solvent was removed under
vacuum. Diethyl ether (200 mL) and saturated aqueous NaHCO3
(50 mL) were added. The organic layer was separated, washed with
saturated aqueous NaCl, and dried over anhydrous Na2SO4. After
evaporation of the solvent, the residue was purified by flash column
chromatography over silica gel using ethyl acetate-hexane (1:3)
as the eluent to afford 3 as white solid (1.98 g; 90% yield): 1H
NMR (400 MHz, CD3OD) δ 7.43 (s, 1H), 6.63 (dd, J ) 6.0, 8.2
Hz, 1H), 5.41 (m, 1H), 4.33-4.36 (m, 2H), 4.23 (m, 1H), 4.09 (s,
3H), 2.78-2.94 (m, 2H), 2.57-2.70 (m, 2H), 2.50-2.57 (ddd, J
) 2.3, 6.0, 14.2 Hz, 1H), 1.17-1.24 (m, 18H); 13C NMR (100
MHz, CD3OD) δ 178.3, 177.8, 177.5, 164.3, 153.3, 152.8, 128.6,
105.2, 85.3, 83.3, 75.8, 65.0, 54.4, 51.8, 38.2, 36.8, 35.2, 35.1, 19.9,
19.3-19.5 (four peaks); HRMS (FAB+) calcd for C24H34O7N4I
(M + H+) 617.1472, found 617.1464.
2-Amino-6-methoxy-7-iodo-9-(â-D-2′-deoxyribofuranosyl)-7-
deazapurine (4). Compound 3 (1.98 g; 3.21 mmol) was dissolved
in 0.5 M methanolic CH3ONa (50 mL) and stirred at 65 °C for 12
h. Saturated aqueous NaHCO3 (20 mL) was added, and the mixture
was stirred for 10 min. Then most of methanol was evaporated,
and the residue was extracted by ethyl acetate (150 mL). The
organic layer was washed with saturated aqueous NaHCO3 and
NaCl, respectively, and dried over anhydrous Na2SO4. After
evaporation of the solvent, the residue was purified by flash column
chromatography over silica gel using CH3OH-CH2Cl2 (1:30-15)
as the eluent to afford 4 as a white solid (1.23 g; 94% yield): 1H
NMR (400 MHz, CD3OD) δ 7.17 (s, 1H), 6.36 (dd, J ) 6.0, 8.4
Hz, 1H), 4.47 (m, 1H), 3.99 (s, 3H), 3.96 (m, 1H), 3.77 (dd, J )
3.4, 12.0 Hz, 1H), 3.70 (dd, J ) 3.7, 12.0 Hz, 1H), 2.55-2.64
(ddd, J ) 6.0, 8.4, 13.4 Hz, 1H), 2.20-2.26 (ddd, J ) 2.4, 5.9,
13.4 Hz, 1H); 13C NMR (100 MHz, CD3OD) δ 164.7, 160.6, 154.3,
126.5, 101.6, 88.7, 86.0, 73.0, 63.7, 53.7, 51.3, 41.1; HRMS
(FAB+) calcd for C12H16O4N4I (M + H+) 407.0216, found
407.0213.
2-Amino-6-methoxy-7-iodo-9-[â-D-5′-O-(tert-butyldimethyl-
silyl)-2′-deoxyribofuranosyl]-7-deazapurine (5). To a stirred
solution of 4 (1.23 g; 3.02 mmol) and imidazole (494 mg; 7.24
mmol) in anhydrous DMF (15 mL) was added tert-butyldimethyl-
silyl chloride (TBDMSCl) (545 mg; 3.51 mmol). The reaction
mixture was stirred at room temperature for 20 h. Then most solvent
was removed under vacuum, and the residue was purified by flash
column chromatography over silica gel using ethyl acetate-hexane
(1:2∼0.5) as the eluent to afford 5 as a white foam (1.38 g; 88%
yield): 1H NMR (400 MHz, CD3OD) δ 7.23 (s, 1H), 6.49 (dd, J
) 6.1, 7.7 Hz, 1H), 4.46 (m, 1H), 3.99 (s, 3H), 3.94 (m, 1H), 3.79-
3.87 (m, 2H), 2.36-2.44 (ddd, J ) 5.8, 7.7, 13.3 Hz, 1H), 2.24-
2.31 (ddd, J ) 3.1, 6.0, 13.3 Hz, 1H), 0.96 (s, 9H), 0.14 (s, 3H),
0.13 (s, 3H); 13C NMR (100 MHz, CD3OD) δ 164.6, 160.7, 154.7,
125.1, 101.0, 88.2, 84.2, 72.7, 64.7, 53.7, 51.7, 41.9, 26.7, 19.4,
-5.0, -5.1; HRMS (FAB+) calcd for C18H30O4N4SiI (M + H+)
521.1081, found 521.1068.
2-Amino-6-methoxy-7-iodo-9-[â-D-3′-O-allyl-5′-O-(tert-butyl-
dimethylsilyl)-2′-deoxyribofuranosyl]-7-deazapurine (6). To a
stirred solution of 5 (1.38 g; 2.66 mmol) in CH2Cl2 (80 mL) were
added tetrabutylammonium bromide (TBAB) (437 mg; 1.33 mmol),
allyl bromide (1.85 mL, 21.4 mmol), and 40% aqueous NaOH
solution (40 mL). The reaction mixture was stirred at room
temperature for 1 h. Ethyl acetate (200 mL) was added, and the
organic layer was separated. The aqueous layer was extracted with
ethyl acetate (2 × 50 mL). The combined organic layer was washed
with saturated aqueous NaHCO3 and NaCl, respectively, and dried
over anhydrous Na2SO4. After evaporation of the solvent, the
residue was purified by flash column chromatography over silica
gel using ethyl acetate-hexane (1:3) as the eluent to afford 6 as a
white solid (1.37 g; 92% yield): 1H NMR (400 MHz, CD3OD) δ
7.20 (s, 1H), 6.43 (dd, J ) 6.2, 7.9 Hz, 1H), 5.89-5.99 (m, 1H),
5.29-5.35 (dm, J ) 17.3 Hz, 1H), 5.16-5.21 (dm, J ) 10.5 Hz,
1H), 4.24 (m, 1H), 4.01-4.11 (m, 3H), 3.99 (s, 3H), 3.76-3.84
(m, 2H), 2.32-2.44 (m, 2H), 0.95 (s, 9H), 0.14 (s, 3H), 0.13 (s,
3H); 13C NMR (100 MHz, CDCl3) δ 163.3, 158.6, 153.6, 134.1,
123.7, 116.9, 100.6, 84.4, 83.0, 79.1, 70.0, 63.6, 53.3, 51.1, 38.1,
26.1, 18.5, -5.1, -5.3; HRMS (FAB+) calcd for C21H34O4N4SiI
(M + H+) 561.1394, found 561.1390.
2-Amino-6-methoxy-7-{3-[(trifluoroacetyl)amino]prop-1-
ynyl]-9-[â-D-3′-O-allyl-5′-O-(tert-butyldimethylsilyl)-2′-deoxyribo-
furanosyl}-7-deazapurine (7). To a stirred solution of 6 (1.37 g;
2.45 mmol) in anhydrous DMF (11 mL) were added tetrakis-
(triphenylphosphine)palladium(0) (286 mg; 0.245 mmol) and CuI
(101 mg; 0.532 mmol). The solution was stirred at room temperature
for 10 min. Then N-propargyltrifluoroacetamide (1.12 g; 7.43 mmol)
and triethylamine (0.68 mL; 4.90 mmol) were added. The reaction
was stirred at room temperature for 13 h with exclusion of air and
light. Most DMF was removed under vacuum, and the residue was
dissolved in ethyl acetate (100 mL). The solution was washed with
saturated aqueous NaHCO3 and NaCl, respectively, and dried over
anhydrous Na2SO4. After evaporation of the solvent, the residue
was purified by flash column chromatography over silica gel using
ethyl acetate-hexane (1:3-1.5) and CH3OH-CH2Cl2 (1:30),
respectively, as the eluent to afford 7 as yellow solid (1.34 g; 94%
yield): 1H NMR (400 MHz, CD3OD) δ 7.34 (s, 1H), 6.42 (dd, J
) 6.2, 7.7 Hz, 1H), 5.88-5.99 (m, 1H), 5.28-5.35 (dm, J ) 17.3
Hz, 1H), 5.16-5.21 (dm, J ) 10.5 Hz, 1H), 4.29 (s, 2H), 4.24 (m,
1H), 4.00-4.09 (m, 3H), 3.98 (s, 3H), 3.76-3.84 (m, 2H), 2.32-
2.45 (m, 2H), 0.94 (s, 9H), 0.12 (s, 3H), 0.11 (s, 3H); 13C NMR
(100 MHz, CD3OD) δ 165.0, 161.2, 158.1 (q, J ) 36 Hz), 154.2,
135.6, 125.0, 117.2 (q, J ) 284 Hz), 117.0, 99.2, 97.3, 86.0, 84.6,
84.5, 80.3, 78.0, 71.0, 64.8, 53.8, 39.0, 30.9, 26.5, 19.3, -5.1, -5.2;
HRMS (FAB+) calcd for C26H37O5N5F3Si (M + H+) 584.2516,
found 584.2491.
3′-O-Allyl-7-{3-[(trifluoroacetyl)amino]prop-1-ynyl}-7-deaza-
2′-deoxyguanosine (8). To a stirred solution of 7 (1.34 g; 2.30
mmol) in anhydrous CH3CN (86 mL) were added NaI (363 mg;
2.42 mmol) and chlorotrimethylsilane (TMSCl) (0.306 mL; 2.42
mmol). The reaction was stirred at room temperature for 1 h and
then at 50 °C for 12 h. The solvent was evaporated, and the residue
was dissolved in anhydrous THF (76 mL). Tetrabutylammonium
fluoride (TBAF) (1 M) in THF solution (4.80 mL; 4.80 mmol) was
added, and the reaction was stirred at room temperature for 1 h.
The solvent was evaporated, and the residue was dissolved in ethyl
acetate (150 mL). The solution was washed with saturated aqueous
NaCl and dried over anhydrous Na2SO4. After evaporation of the
solvent, the residue was purified by flash column chromatography
over silica gel using CH3OH-ethyl acetate (1:30) as the eluent to
afford 8 as yellow solid (356 mg; 34% yield): 1H NMR (400 MHz,
CD3OD) δ 7.21 (s, 1H), 6.30 (dd, J ) 6.0, 8.4 Hz, 1H), 5.88-5.99
(m, 1H), 5.28-5.35 (dm, J ) 17.3 Hz, 1H), 5.15-5.20 (dm, J )
10.5 Hz, 1H), 4.29 (s, 2H), 4.23 (m, 1H), 4.00-4.10 (m, 3H), 3.65-
3.75 (m, 2H), 2.41-2.49 (ddd, J ) 5.8, 8.4, 13.6 Hz, 1H), 2.34-
2.40 (ddd, J ) 2.3, 6.0, 13.6 Hz, 1H); 13C NMR (100 MHz,
CD3OD) δ 160.9, 158.0 (q, J ) 36 Hz), 154.1, 151.8, 135.6, 124.4,
117.2 (q, J ) 284 Hz), 117.0, 101.4, 99.7, 86.4, 85.5, 84.8, 80.7,
78.0, 71.0, 63.7, 38.5, 31.2; HRMS (FAB+) calcd for C19H21O5N5F3
(M + H+) 456.1495, found 456.1493.
3′-O-Allyl-7-(3-aminoprop-1-ynyl)-7-deaza-2′-deoxyguanosine-
5′-triphosphate (9). The procedure is the same as that of preparing
3′-O-allyl-5-(3-aminoprop-1-ynyl)-2′-deoxyuridine-5′-triphos-
phate in ref 2 to yield 9 as a colorless syrup: 1H NMR (300 MHz,
D2O) δ 7.56 (s, 1H), 6.37 (t, J ) 7.3 Hz, 1H), 5.89-6.02 (m, 1H),
5.31-5.39 (dm, J ) 17.3 Hz, 1H), 5.21-5.28 (dm, J ) 10.5 Hz,
1H), 4.49 (s, 2H), 4.32 (m, 1H), 4.06-4.18 (m, 3H), 3.92-3.99
(m, 2H), 2.44-2.60 (m, 2H);31P NMR (121.4 MHz, D2O) δ -6.1
(d, J ) 20.8 Hz, 1P), -10.8 (d, J ) 18.9 Hz, 1P), -21.9 (t, J )
19.8 Hz, 1P).
3′-O-Allyl-dGTP-PC-Bodipy-FL-510 (10). PC-Bodipy-FL-510
NHS ester (prepared by the same procedure as in ref 9) (7.2 mg,
12 µmol) in 300 µL of acetonitrile was added to a solution of 9 (2
mg, 3.4 µmol) in 300 µL of Na2CO3-NaHCO3 aqueous buffer (0.1
J. Org. Chem, Vol. 71, No. 8, 2006 3251

Meng et al.
M, pH 8.5). The reaction mixture was stirred at room temperature
for 3 h. A preparative silica gel TLC plate was used to separate
the unreacted PC-Bodipy-FL-510 NHS ester from the fraction
containing 10 with CHCl3-CH3OH (85:15) as the eluent. The
product was concentrated further under vacuum and purified with
reversed-phase HPLC on a 150 × 4.6-mm C18 column to obtain
the pure product 10 (retention time of 34 min). Mobile phase: A,
8.6 mM triethylamine/100 mM hexafluoroisopropyl alcohol in water
(pH 8.1); B, methanol. Elution was performed with 100% A
isocratic over 10 min, followed by a linear gradient of 0-50% B
for 20 min and then 50% B isocratic over another 20 min. 3′-O-
Allyl-dGTP-PC-Bodipy-FL-510 10 was characterized by the fol-
lowing primer extension reaction and characterization by MALDI-
TOF MS.
Primer Extension Using 3′-O-Allyl-dGTP-PC-Bodipy-FL-510
(10) and Photocleavage of the Extension Product 11. The
polymerase extension reaction mixture consisted of 60 pmol of
primer (5′-GTTGATGTACACATTGTCAA-3′), 80 pmol of
100-mer template (5′-TACCCGGAGGCCAAGTACGGCGGG-
T A C G T C C T T G A C A A T G T G T A C A T C A A C A T -
C A C C T A C C A C C A T G T C A G T C T C G G T T G -
GATCCTCTATTGTGTCCGGG-3′), 120 pmol of 3′-O-allyl-
dGTP-PC-Bodipy-FL-510, 1X Thermopol reaction buffer (20 mM
Tris-HCl/10 mM (NH4)2SO4/10 mM KCl/2 mM MgSO4/0.1%
Triton X-100, pH 8.8, New England Biolabs), and 6 units of 9°N
Polymerase (exo-)A485L/Y409V in a total volume of 20 µL. The
reaction consisted of 20 cycles at 94 °C for 20 s, 46 °C for 40 s,
and 60 °C for 90 s. After the reaction, a small portion of the DNA
extension product was desalted by using ZipTip and analyzed by
MALDI-TOF MS, which shows a dominant peak at m/z 7048
corresponding to the DNA product 11. The rest of the product
mixture was freeze-dried, resuspended in 200 µL of deionized water,
and irradiated at 355 nm for 10 s to cleave the fluorophore from
the DNA to yield product 12 and then analyzed by MALDI-TOF
MS (m/z 6552).
10 mM KCl/2 mM MgSO4/0.1% Triton X-100, pH 8.8, 1 µL),
Na2PdCl4 in degassed H2O (7 µL, 23 nmol), and P(PhSO3Na)3 in
degassed H2O (10 µL, 176 nmol) to perform the deallylation. The
reaction mixture was then placed in a heating block and incubated
at 70 °C for 30 s to yield quantitatively deallylated DNA product
13 and analyzed by MALDI-TOF MS (m/z 6512).
Primer Extension Reaction Performed with the Deallylated
DNA Product. The deallylated DNA product 13 was used as a
primer in a single-base extension reaction. The 20 µL: reaction
mixture consisted of 60 pmol of the deallylated product 13, 80 pmol
of the 100-mer template (5′-TACCCGGAGGCCAAGTACGGC-
GGGTACGTCCTTGACAATGTGTACATCAACATCACCTACCA-
CCATGTCAGTCTCGGTTGGATCCTCTATTGTGTCCGGG-3′),
120 pmol of 3′-O-allyl-dGTP-PC-Bodipy-FL-510 (10), and 6 units
of 9°N Polymerase (exo-)A485L/Y409V in a total volume of 20
µL. The reaction consisted of 20 cycles at 94 °C for 20 s, 46 °C
for 40 s, and 60 °C for 90 s. The DNA extension product 14 was
desalted by using the ZipTip protocol, and a small portion was
analyzed by using MALDI-TOF MS (m/z 7429). The remaining
product was then irradiated with near-UV light (355 nm) for 10 s
to cleave the fluorophore from the extended DNA product. The
resulting photocleavage product 15 (m/z 6933) was analyzed by
using MALDI-TOF MS. Finally, deallylation of the photocleavage
product 15 was performed using a Pd-catalyzed deallylation reaction
resulting in a deallylated DNA product 16, which was then analyzed
by MALDI-TOF MS (m/z 6893).
Acknowledgment. We thank New England Biolabs for
providing the 9°N DNA polymerase. This work was supported
by NIH Grant Nos. P50 HG002806 and R01 HG003582 and
the Packard Fellowship for Science and Engineering.
Supporting Information Available: Spectral data for 2-9
(1H, 13C, and 31P NMR) and general experimental procedures.
This material is available free of charge via the Internet at
http://pubs.acs.org.
Deallyation of Photocleaved DNA Extension Product 12. DNA
product 12 (20 pmol) was added to a mixture of degassed 1X
Thermopol reaction buffer (20 mM Tris-HCl/10 mM (NH4)2SO4/
JO060300K
3252 J. Org. Chem., Vol. 71, No. 8, 2006