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Nucleic Acids Research 2005 33(5):1532-1543; doi:10.1093/nar/gki293
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Published online 14 March 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Hybridization properties and enzymatic replication of oligonucleotides containing the photocleavable 7-nitroindole base analog

Caroline Crey-Desbiolles, Nathalie Berthet*, Mitsuharu Kotera and Pascal Dumy

LEDSS UMR 5616 CNRS, ICMG FR2607, Université Joseph Fourier BP53, 38041 Grenoble Cédex 9, France

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

Received December 13, 2004. Revised February 21, 2005. Accepted February 21, 2005.

Universal DNA base analogs having photocleavable properties would be of great interest for development of new nucleic acid fragmentation tools. The photocleavable 7-nitroindole 2'-deoxyribonucleoside d(7-Ni) was previously shown to furnish a highly efficient approach to photochemically trigger DNA backbone cleavage at preselected position when inserted in a DNA fragment. In the present report, we examine its potential use as universal DNA nucleoside, by analogy with the 5-nitroindole analog that is generally considered as universal base. The d(7-Ni) phosphoramidite was incorporated into oligonucleotides. Hybridization properties of resulting 11mer duplexes indicated a behavior close to that of the 5-nitroindole analog. Enzymatic recognition by Klenow fragment exonuclease-free using 40mers containing the unnatural bases as templates indicated notably a decrease of the polymerase activity with preferential incorporation of dAMP opposite both the 7-Ni and 5-Ni bases. Incorporation of the d(7-Ni) triphosphate was also studied indicating absence of significant differences between the incorporation kinetics opposite each natural base in the template. All the hybridization and enzymatic data indicate that 7-nitroindole can be considered as a cleavable base analog, although not strictly fulfilling, like the 5-nitro isomer, all properties required for a universal base.


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N. Berthet, C. Crey-Desbiolles, M. Kotera, and P. Dumy
Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2'-deoxyadenosine mimic
Nucleic Acids Res., September 1, 2009; 37(16): 5237 - 5245.
[Abstract] [Full Text] [PDF]


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