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Nucleic Acids Research Advance Access published online on July 8, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp562
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Chemistry and Synthetic Biology

Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2'-deoxyadenosine mimic

Nathalie Berthet1,*, Caroline Crey-Desbiolles1, Mitsuharu Kotera2 and Pascal Dumy1

1Département de Chimie Moléculaire-Equipe Ingénierie et Interactions BioMoléculaires, UMR-5250, ICMG FR-2607, CNRS, Université Joseph Fourier, BP53, 38041 Grenoble Cedex 9 and 2Laboratoire de Chimie Génétique, Associé CNRS/Université Louis Pasteur de Strasbourg, Faculté de Pharmacie, BP 24, 67401 Illkirch, France

*To whom correspondence should be addressed. Tel: +33 476 514430; Fax: +33 476 514946; Email: Nathalie.Berthet{at}ujf-grenoble.fr

Received March 24, 2009. Revised June 8, 2009. Accepted June 17, 2009.

The phototriggered cleavage of chemical bonds has found numerous applications in biology, particularly in the field of gene sequencing through photoinduced DNA strand scission. However, only a small number of modified nucleosides that are able to cleave DNA at selected positions have been reported in the literature. Herein, we show that a new photoactivable deoxyadenosine analogue, 3-nitro-3-deaza-2'-deoxyadenosine (d(3-NiA)), was able to induce DNA backbone breakage upon irradiation ({lambda} > 320 nm). The d(3-NiA) nucleoside was chemically incorporated at desired positions into 40-mer oligonucleotides as a phosphoramidite monomer and subsequent hybridization studies confirmed that the resulting modified duplexes display a behaviour that is close to that of the related natural sequence. Enzymatic action of the Klenow fragment exonuclease free revealed the preferential incorporation of dAMP opposite the 3-NiA base. On the other hand, incorporation of the analogous 3-NiA triphosphate to a primer revealed high enzyme efficiency and selectivity for insertion opposite thymine. Furthermore, only the enzymatically synthesized base pair 3-NiA:T was a substrate for further extension by the enzyme. All the hybridization and enzymatic data indicate that this new photoactivable 3-NiA triphosphate can be considered as a photochemically cleavable dATP analogue.


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