Click-click-click: Single to triple modification of DNA

Article abstract of DOI:10.1002/anie.200705664

(Chemical Presented) One, two, or three: An efficient, modular, and robust protocol has been developed for the multiple functionalization of DNA. It is based on the click reaction of azides with the alkyne substituents on an oligodeoxyribonucleotide (ODN)

Full text of DOI:10.1002/anie.200705664

Communications
DOI: 10.1002/anie.200705664
DNA Labeling
Click–Click–Click: Single to Triple Modification of DNA**
Philipp M. E. Gramlich, Simon Warncke, Johannes Gierlich, and Thomas Carell*
The attachment of labels such as fluorescent dyes or biotin
molecules to DNA is of paramount importance for DNA-
based molecular diagnostics[1] and for nanotechnological
applications.[2,3] There is high demand for such modified
oligonucleotides, but the chemistry behind the labeling
procedures is cumbersome, and the modified oligonucleotides
are frequently obtained in only low yields. Presently, the
labels are incorporated as the corresponding phosphorami-
dites[4] during the solid-phase synthesis of oligonucleotides,
which frequently reduces the coupling yield significantly. This
method is restricted to labels that can withstand the harsh
conditions of DNA synthesis and deprotection. Alternatively,
the labels are introduced postsynthetically[5] by, for example,
reaction of the corresponding activated esters with amino-
alkyl-modified oligonucleotides.[6] This method suffers from
inefficient coupling yields, making the purification of the
labeled oligonucleotides a challenging task.
of oligonucleotides. We thought that the best way to achieve
this goal would be to introduce one free alkyne for the first
click reaction and second TMS-protected alkyne
a
(Scheme 1) for the second click process after removal of the
In a world in which the demand for labeled oligonucleo-
tides is rapidly growing, new methods for the efficient
incorporation of multiple different labels are required. Seela
and Sirivolu[7] and our group[2,8] have recently discovered that
the copper(I)-catalyzed version of the azide–alkyne reaction
to give triazoles, developed by Meldal et al.[9] and Sharpless
et al.[10] can be used to functionalize alkyne-modified DNA
nucleobases with extremely high efficiency. A critical point is
the presence of a sufficient amount of a proper copper(I)-
complexing ligand[11] to prevent the copper-catalyzed cleav-
age of DNA.[12] Herein we report that this chemistry can be
extended to label oligonucleotides with up to three (and
possibly more) different labels. These functionalizations can
be achieved either directly on the resin[13] or in solution after
deprotection of the oligonucleotide. The latter method can be
used to incorporate extremely sensitive labels with unprece-
dented efficiency.
Scheme 1. Phosphoramidites 1 and 2. DMT=4,4’-dimethoxytriphenyl-
methyl, TMS=trimethylsilyl, TIPS=triisopropylsilyl, Bz=benzoyl.
TMS group with mild acid on the resin. To test the feasibility
of a click reaction on the resin we prepared a test strand
containing the base derived from alkyne 1 and performed the
click reaction directly on the resin, followed by DNA
deprotection. Comparison of the HPLC trace of the func-
tionalized DNA strand with that of an untreated DNA strand
of the same series showed virtually quantitative conversion
proving that the click reaction proceeded with extremely high
efficiency directly on the controlled pore glass (CPG) support
used for DNA synthesis (data not shown).
To introduce two labels, we incorporated the thymidine
and the cytidine building blocks 1 and 2a into oligonucleo-
tides such as ODN-1 and ODN-2 (Table 1) using standard
The first goal was to establish a method for the introduc-
tion of two different labels[14] during the solid-phase synthesis
Table 1: ODNs employed in this study.[a]
[*] Dipl.-Chem. P. M. E. Gramlich, Dipl.-Chem. S. Warncke,
Dr. J. Gierlich, Prof. Dr. T. Carell
ODN
Sequence
ODN-1
ODN-2
ODN-3
ODN-4
5’-GCGCXGTTCATTYGCG-3’
5’-CGCYACACGAAXCCG-3’
5’-GCGCZGTTCATTXGCG-3’
5’-GCGCYGTTXATTZCGC-3’
Department Chemie und Biochemie
Ludwig-Maximilians-Universität
Butenandtstrasse 5-13, 81377 München (Germany)
Fax: (+49)89-2180-77756
E-mail: thomas.carell@cup.uni-muenchen.de
[a] X=DNA nucleotide based on 1, Y=DNA nucleotide based on 2a,
Z=DNA nucleotide based on 2b.
[**] P.M.E.G. thanks the Cusanuswerk for a PhD scholarship. J.G. thanks
the Fonds der chemischen Industrie for a PhD scholarship. We
thank Dr. G. Clever for the preparation of the anthraquinone azides
and pyrene azides. The work was supported by the Fonds der
Chemischen Industrie and the Deutsche Forschungsgemeinsschaft
(SFB 749 and SFB 486). Support bythe Excellence Cluster NIM
(Nanoinitiative Munich) is greatlyappreciated.
phosphoramidite chemistry. The coupling yields of both
phosphoramidites were excellent. After full assembly of the
oligonucleotide on the solid support, the resin was dried and
the first click reaction was performed by shaking the resin
with a solution of CuBr, tris(benzyltriazolylmethyl)amine
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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Angewandte
Chemie
Table 2: Postsynthetic labeling of ODNs 1–4.[d]
(TBTA),[11] sodium ascorbate, and benzyl azide (3;
Scheme 2). The resin was washed and rinsed with 1% acetic
acid to cleave the TMS protecting group on the second
[a]
EntryDNA
Label 1
Label 2
Label 3
Yield [%]
1
2
3
4
5
6
7
8
ODN-1
ODN-2
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-3
ODN-4
ODN-4
3*
3*
5
4
4
3
3
3
3
8
9
9
9
10
8
3*
3*
8*
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
7
5
[b]
75[c]
67
59
59
70
85
67
66
83
92
62
90
4
4
6
7
5
4
7
9
4
3
5
4
5
11
8
7
9
10
11
12
13
14
15
16
17
74
58
45[c]
52[c]
[a] Determined byintegration of the HPLC trace of the crude product at
260 nm after the last click reaction. [b] n.a. [c] HPLC purification after the
click reaction on the resin. [d] Click reaction performed on resin.
one clicked-on modification and one free alkyne, was
subjected to the second click reaction in solution (CuBr,
TBTA, azide 4), yielding the doubly modified DNA in
excellent yields and purity (Table 2, entry 2).
The previously unmet challenge was to prepare oligonu-
cleotides modified with two sensitive molecules. This can be
readily achieved with the building blocks 1 and 2b, which
were incorporated into ODN-3 (Table 1) using standard
phosphoramidite chemistry. After deprotection and cleavage
of the oligonucleotide from the resin, the first click reaction
was performed (using the solution conditions reported above)
yielding the singly modified oligonucleotide with the
expected high yield of > 90% on average and full retention
of the TIPS protecting group. For the second click step we
cleaved the TIPS protecting group with a solution of
tetrabutylammonium fluoride (TBAF) in acetonitrile/DMF
(4:1 v/v) without causing any damage to the DNA. The
second click reaction in solution yielded the doubly modified
oligonucleotides in excellent yields (60–90% over three
steps). We performed the double click with a whole series
of different labels and always observed excellent yields
(Table 2, entries 3–15). It is worth mentioning that in all
cases simple precipitation of the product from ethanol after
each reaction step was sufficient for purification. Figure 1
shows a typical HPLC chromatogram and a MALDI-TOF
spectrum of the crude product obtained after a double
modification of ODN-3. For very sensitive applications one
final HPLC purification is recommended. In rare cases, such
as for Cy3 azide 12, we found that the linker was cleaved to a
small extent, making the development of a more stable linker
necessary.
Scheme 2. Azide building blocks used.
alkyne. Then the second click reaction was performed
analogously to the first one using azide 8. The DNA was
finally cleaved from the resin, and all protecting groups were
removed by exposing the resin to ammonia in H2O/EtOH
(3:1). The MALDI-TOF spectrum obtained for the crude
product was in full agreement with the expected mass of the
doubly modified oligonucleotide (Table 2, entry 1 and
Supporting Information), showing that two stable labels can
be introduced into DNA directly on the solid support.
To test the functionalization of oligonucleotides with
labels too unstable to survive the harsh cleavage conditions,
we next performed the second click reaction in solution after
oligonucleotide deprotection. Treatment of the singly modi-
fied ODN-2 (Table 1) with conc. NH3 in water/ethanol
cleaved the DNA from the resin. Under these conditions
the base protecting groups and the TMS group on the second
alkyne were removed as well. The obtained DNA, bearing
Using the click reaction followed by precipitation of the
product from ethanol, it was also possible to modify
oligonucleotides with three different labels. To this end, we
introduced the building blocks 1, 2a, and 2b into oligonu-
cleotides such as ODN-4 (Table 1). The first click reaction
was performed directly on the resin. The singly modified
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Communications
DNA. The efficiency of the method is based on three
observations: 1. The TMS protecting group is quantitatively
removed with ammonia during DNA deprotection. 2. The
TIPS-protected alkyne is quantitatively retained during this
ammonia treatment. 3. The TIPS protecting group can be
removed efficiently and mildly. We believe that the chemistry
presented here can change the way in which modified
oligonucleotides are prepared.
Received: December 11, 2007
Published online: March 28, 2008
Keywords: alkynes · azides · click chemistry · cycloaddition ·
.
DNA labeling
Figure 1. HPLC trace (260 nm) of the crude product ODN-3 modified
with 8 and 4 (Table 2, entry10) and the corresponding MALDI-TOF
spectrum (inset).
[1] D. M. Hammond, A. Manetto, J. Gierlich, V. A. Azov, P. M. E.
Gramlich, G. A. Burley, M. Maul, T. Carell, Angew. Chem. 2007,
119, 4262; Angew. Chem. Int. Ed. 2007, 46, 4184.
[2] G. A. Burley, J. Gierlich, M. R. Mofid, S. T. H. Nir, Y. Eichen, T.
Carell, J. Am. Chem. Soc. 2006, 128, 1398.
[3] J. J. Storhoff, C. A. Mirkin, Chem. Rev. 1999, 99, 1849; Q. Gu, C.
Cheng, R. Gonela, S. Suryanarayanan, S. Anabathula, K. Dai,
D. T. Haynie, Nanotechnology 2006, 17, R14.
[4] C. Wagner, H.-A. Wagenknecht, Chem. Eur. J. 2005, 11, 1871; S.
Kodama, S. Asano, T. Moriguchi, H. Sawai, K. Shinozuka,
Bioorg. Med. Chem. Lett. 2006, 16, 2685.
[5] J. A. Prescher, C. R. Bertozzi, Nat. Chem. Biol. 2005, 1, 13.
[6] L. M. Smith, S. Fung, M. W. Hunkapiller, T. J. Hunkapiller, L. E.
Hood, Nucleic Acids Res. 1985, 13, 2399.
[7] F. Seela, V. R. Sirivolu, Chem. Biodiversity 2006, 3, 509.
[8] J. Gierlich, G. A. Burley, P. M. E. Gramlich, D. M. Hammond, T.
Carell, Org. Lett. 2006, 8, 3639.
[9] C. W. Tornoe, C. Christensen, M. Meldal, J. Org. Chem. 2002, 67,
3057.
[10] V. V. Rostovtsev, L. G. Green, V. V. Fokin, K. B. Sharpless,
Angew. Chem. 2002, 114, 2708; Angew. Chem. Int. Ed. 2002, 41,
2596.
[11] T. R. Chan, R. Hilgraf, K. B. Sharpless, V. V. Fokin, Org. Lett.
2004, 6, 2853.
oligonucleotide was subsequently cleaved from the support
under concomitant cleavage of the TMS group and then
purified by HPLC. The second click reaction was performed
in solution with the expected high yield. Precipitation of the
doubly modified oligonucleotide from ethanol, cleavage of
the TIPS group with TBAF, and a subsequent third click
reaction in solution furnished the desired triply modified
oligonucleotides after a final precipitation in yields of about
50% (Table 2, entries 16 and 17).
Labeling of oligonucleotides directly at certain bases
(here dC and dT) is highly desirable, but the introduction of
labels outside the nucleobases, for example, on the phos-
phates or the sugars is also frequently needed. For this, we
prepared the alkyne-bearing nonnucleoside DNA modifiers
13 and 14 (Scheme 3). Click reactions using these building
blocks in DNA worked just as efficiently.[15]
[12] C. J. Burrows, J. G. Muller, Chem. Rev. 1998, 98, 1109; S.
Thyagarajan, N. N. Murthy, A. A. N. Sarjeant, K. D. Karlin, S. E.
Rokita, J. Am. Chem. Soc. 2006, 128, 7003.
[13] F. Seela, V. R. Sirivolu, Helv. Chim. Acta 2007, 90, 535; C.
Bouillon, A. Meyer, S. Vidal, A. Jochum, Y. Chevolot, J.-P.
Cloarec, J.-P. Praly, J.-J. Vasseur, F. Morvan, J. Org. Chem. 2006,
71, 4700.
[14] V. Aucagne, D. A. Leigh, Org. Lett. 2006, 8, 4505.
[15] D. I. Rozkiewicz, J. Gierlich, G. A. Burley, K. Gutsmiedl, T.
Carell, B. J. Ravoo, D. N. Reinhoudt, ChemBioChem 2007, 8,
1997.
Scheme 3. Nonnucleoside DNA modifiers 13 and 14.
In summary, we have developed a highly efficient,
modular, and robust multiple functionalization protocol for
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Angew. Chem. Int. Ed. 2008, 47, 3442 –3444