Direct polymerase synthesis of reactive aldehyde-functionalized DNA and Its conjugation and staining with hydrazines

Article abstract of DOI:10.1002/anie.200905556

(Figure Presented) Reactive aldehyde-modified DNA was prepared in two steps by Suzuki crosscoupling of halogenated nucleoside triphosphates (dNTPs) with 4-formylthiophene-2-boronic acid and subsequent polymerase incorporation of the modified nucleotides i

Full text of DOI:10.1002/anie.200905556

Communications
DOI: 10.1002/anie.200905556
Functionalized DNA
Direct Polymerase Synthesis of Reactive Aldehyde-Functionalized
DNA and Its Conjugation and Staining with Hydrazines**
ˇ
Veronika Raindlovꢀ, Radek Pohl, Miloslav Sanda, and Michal Hocek*
Apart from a wide range of novel applications of function-
alized DNA in chemical biology, nanotechnology, and mate-
rial sciences,[1] attachment of reactive functional groups to
nucleic acids is needed for further transformations or
bioconjugates. The introduction of alkyne, azide, or diene
groups either by chemical phosphoramidite synthesis or by
enzymatic polymerase synthesis has been achieved and the
modified DNA was used for click-chemistry,[2,3] Staudinger
ligation,[4] and Diels–Alder reactions.[5] An aldehyde func-
tional group is a very attractive group because of its high and
specific reactivity with diverse reagents. However, it was
considered too reactive and fragile to be incorporated directly
(chemically or enzymatically)[6] and the few successful
examples were prepared indirectly by a click reaction with
azide derivatives of reducing sugars,[3] or by introduction of
2,3-dihydroxypropyl or 3,4-dihydroxypyrrolidine moieties[7,8]
and subsequent oxidative cleavage of the vicinal diols to
(di)aldehydes. The syntheses of the nucleoside/nucleotide
monomers were laborious multistep procedures and addi-
tional post-synthetic steps were required to release the
aldehyde function in DNA.[7,8] Metallization[7] or interstrand
cross-linking[8] were demonstrated to be very useful applica-
tions of aldehyde-modified oligonucleotides (ONs) or DNA.
Therefore we decided to develop a simple and efficient direct
protocol for construction of aldehyde-modified DNA by
application of our two-step (cross-coupling polymerase incor-
poration) method.[9,10] In addition, we wished to develop a
methodology for additional conjugation and staining of
aldehyde-modified DNA by hydrazone formation.
phate). Commercially available 5-formylthiophene-2-boronic
acid was selected as a suitable carrier for the aldehyde group,
and its aqueous-phase cross-coupling with monophosphate 1
proceeded within 40 minutes and gave aldehyde-modified
dCMP 2 in 50% yield (Scheme 1). The next task was the
formation of the hydrazone species, which is usually only
performed in dry organic solvents (owing to the formation of
water in the reaction). To make the reaction amenable to
aqueous conditions, we have adapted the protocol developed
by Dawson and co-workers[11] for aqueous conjugation of
peptides, which uses aqueous ammonium acetate and aniline
to facilitate the condensation. To test the reactions with 2, we
selected two arylhydrazines (3 and 4) that are commonly used
as aldehyde-specific dyes.[12,13] The reactions of aldehyde-
nucleotide 2 with 3 or 4 proceeded at room temperature for
approximately 20 hours and gave the corresponding orange
(5) or violet (6) hydrazones, which were fully characterized
(see the Supporting Information). As the formation of
hydrazone in water is inherently a reversible reaction, the
yields for the isolated products of 51 and 31%, respectively,
were acceptable and useful.
The cross-coupling protocol was then applied in the
reactions of iodinated dNTPs (dCITP and dAITP)[10,14] with 5-
formylthiophene-2-boronic acid. The desired aldehyde-modi-
fied dNTPs (dCFTTP and dAFTTP) were isolated in 65 and
41% yields, respectively (Scheme 2).
Next we have tested the polymerase incorporation of
dCFTTP and dAFTTP in primer extension (PEX) or poly-
merase chain reaction (PCR) experiments using several
The methodology of choice involved Suzuki cross-cou-
pling of a halogenated nucleoside triphosphate (dNTP) with
an aldehyde-containing boronic acid, and subsequent poly-
merase incorporation into DNA.[9,10] Furthermore, we wanted
to develop a general methodology for hydrazone formation in
aqueous media. To test the first and last steps of our proposed
route, we performed the reactions on the model compound 5-
iodo-dCMP (1; dCMP = 2’-deoxycytidine-5’-O-monophos-
ˇ
[*] V. Raindlovꢀ, Dr. R. Pohl, M. Sanda, Prof. Dr. M. Hocek
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic, v.v.i.
Flemingovo nam. 2, 16610 Prague 6 (Czech Republic)
Fax: (+420)2-2018-3559
E-mail: hocek@uochb.cas.cz
Homepage: http://www.uochb.cas.cz/hocekgroup
Scheme 1. Synthesis of aldehyde-modified cytidine monophosphate 2,
and subsequent synthesis of colored hydrazone-modified cytidine
monophosphates 5 and 6. Reaction conditions: a) 5-formylthiophene
boronic acid, Pd(OAc)2, TPPTS, Cs2CO3, ACN/H2O (1:2), 120 8C,
40 min, 50%; b) 2,4-dinitrophenylhydrazine (3), NH4OAc, aniline, H2O,
RT, 21 h, 51%; c) 4-(1-methylhydrazino)-7-nitrobenzofurazane (4),
NH4OAc, aniline, H2O, RT, 18 h, under Ar, 31%. TPPTS=3,3’,3’’-
phosphinetriyltris(benzenesulfonic acid) trisodium salt.
[**] This work was supported by the Academy of Sciences of the Czech
Republic (Z4 055 0506), the Ministry of Education (LC512), the
Czech Science Foundation (203/09/0317), and Gilead Sciences, Inc.
(Foster City, CA, USA).
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.200905556.
1064
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Angew. Chem. Int. Ed. 2010, 49, 1064 –1066

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Chemie
increase in stability by 2.58C per modification (see the
Supporting Information).
PCR is even more demanding in terms of efficiency and
fidelity of incorporation and many previous modifications
successful in PEX did not work in PCR.[10] However, the
aldehyde-modified dNFTTPs were excellent substrates even in
PCR reactions. PCR with a 98-mer template (Figure 1b)
proceeded smoothly with Pwo-polymerase-amplified DNA
duplex products containing 37 (AFT) or 34 (CFT) aldehyde
groups. Longer templates (287 and 1162 nt) were also
subjected to PCR with dNFTTPs. When using 287 nt template,
Pwo polymerase did not work, while Vent(exoÀ) gave only
weak amplification. Only the use of KOD XL polymerase[7]
gave efficient amplification with this template (Figure 1c).
Therefore, the KOD XL polymerase was then used for
successful PCR amplification of a long 1162 nt template
(Figure 1d). In both cases, full-length products were detected
with dAFTTP being a somewhat better substrate that gave
more efficient amplification compared to dCFTTP. This out-
come proves the possibility of these modified dNFTTPs to be
of general use in PCR.
The final goal was to apply the methodology for the
synthesis and conjugation of aldehyde-modified DNA with
hydrazines (Figure 2a). The 98-mer PCR product made from
dCFTTP (+ natural dATP, TTP, and dGTP) was treated with
hydrazine 3 or 4. The dinitrophenylhydrazone–DNA was
stained to yellow, while the nitrobenzofurazanehydrazone–
DNA was pink (Figure 2b). The corresponding unmodified
PCR products treated with hydrazine 3 or 4, as well as the
aldehyde-DNAwere colorless. After staining with hydrazines,
the UV/Vis spectra of the modified PCR products were in full
accord with the UV/Vis spectra of isolated and fully
characterized nucleotide hydrazones 5 and 6 (Figure 2c and
the Supporting Information). Recalculated from extinction
coefficients and the Beer–Lambert law, the average number
of hydrazone-modified cytosines was 19 (55%) and 16 (47%),
for B and C (Figure 2) respectively, out of 34 aldehyde groups
in the PCR product. This result is consistent with the yields of
isolated hydrazones 5 and 6. In addition, we have also used
the 98-mer PCR-CFT and PCR-AFT products for Tollens
reaction[7] to further prove the presence and reactivity of the
aldehyde groups. In accord with the literature,[7] this reaction
with aldehyde-modified DNA revealed a time-dependent
increase of absorbance at 450 nm (see Figure S9 in the
Supporting Information).
Scheme 2. Synthesis of aldehyde-modified nucleoside triphosphates.
Reaction conditions: a) 5-formylthiophene boronic acid, Pd(OAc)2,
TPPTS, Cs2CO3, ACN/H2O (1:2), 100 8C, 1 h, 65 and 41%.
polymerases.[15] The question was whether the polymerases
would tolerate the presence of a reactive aldehyde group
(which may even react with some functional groups of the
protein, for example, the amino group of lysine) and
incorporate the dNFTTPs into DNA. The best results were
obtained with Vent(exoÀ) DNA polymerase, which readily
and selectively incorporated both aldehyde-modified nucle-
otides by PEX—even incorporation into sequences contain-
ing multiple modifications (Figure 1a). DyNAzyme and
Phusion polymerases were also efficient in their incorporation
by PEX (see the Supporting Information). Apart from PAGE
analysis with proper negative control experiments, the
formation of aldehyde-modified ON was confirmed by
MALDI analysis of 31-meric product containing four modi-
fied AFT bases (see the Supporting Information). Thermal
denaturation (melting temperature) of 31-meric DNA
duplexes containing four AFT or four CFT bases showed
In conclusion, we have developed the first direct and
efficient methodology for introduction of an aldehyde func-
tional group to DNA in only two steps. The aldehyde group
(attached through a thiophene moiety) withstands both
Suzuki cross-coupling and polymerase incorporation. The
aldehyde-modified dNTPs are excellent substrates for DNA
polymerases and the aldehyde-nucleotides are readily incor-
porated by PEX or PCR to diverse ONs or DNA duplexes
(even in a manifold fashion). We have also developed a simple
aqueous conjugation with arylhydrazines and used this
protocol for DNA staining. Further application of the (now)
easily available aldehyde-modified DNA in conjugation with
other useful hydrazines (fluorescent, redox active, etc.) or
with diverse biomolecules are currently under way.
Figure 1. a) Primer extension with Vent(exoÀ) DNA polymerase. P:
Primer (5’-32P-end labeled primer-template); +: natural dNTPs; C-:
dTTP, dATP, dGTP; A-: dTTP, dCTP, dGTP; CFT: dCFTTP, dTTP, dATP,
dGTP; AFT: dAFTTP, dTTP, dCTP, dGTP. b) PCR synthesis of 98-mer by
Pwo polymerase. Lane 1: ladder; lane 2 (+): natural dNTPs; lane 3
(C-): dTTP, dATP, dGTP; lane 4 (A-): dTTP, dCTP, dGTP; lane 5 (CFT):
dCFTTP, dTTP, dATP, dGTP; lane 6 (AFT): dAFTTP, dTTP, dCTP, dGTP,
c) PCR synthesis of 287-mer by KOD XL polymerase, d) PCR synthesis
of 1162-mer by KOD XL polymerase.
Angew. Chem. Int. Ed. 2010, 49, 1064 –1066
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1065

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Figure 2. a) Synthesis of aldehyde-functionalized DNA followed by
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staining with hydrazines. A: PCR product from all natural dNTPs
treated with 4 (colorless product); B: 98-mer PCR product from three
natural dNTPs and dCFTTP treated with 3 (yellow); C: 98-mer PCR
product from three natural dNTPs and dCFTTP treated with 4 (pink).
c) UV/Vis spectra of unmodified and modified 98-mer PCR products
without or after staining with hydrazines. A, B, and C, Spectra are of
the same solutions as in b), D (green line) is the spectrum of CTF-
containing PCR product without staining (colorless).
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Received: October 5, 2009
Revised: November 18, 2009
Published online: December 29, 2009
Keywords: aldehydes · modified DNA ·
.
nucleoside triphosphates · oligonucleotides ·
polymerase chain reaction
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Angew. Chem. Int. Ed. 2010, 49, 1064 –1066