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Nucleic Acids Research 2005 33(3):1031-1039; doi:10.1093/nar/gki253
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Published online 17 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

8-vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2'-deoxyribosyl-2-aminopurine with improved properties

Nouha Ben Gaied, Nicole Glasser1, Nick Ramalanjaona1, Hervé Beltz1, Philippe Wolff2, Roland Marquet2, Alain Burger and Yves Mély1,*

Laboratoire de Chimie Bioorganique, UMR 6001 du CNRS, Université de Nice Sophia Antipolis Parc Valrose 06108 Nice cedex 2, France 1 Laboratoire de Pharmacologie et Physico-chimie des interactions cellulaires et moléculaires, UMR 7034 du CNRS, Faculté de Pharmacie, Université Louis Pasteur 74 Route du Rhin, BP 24, 67401 Illkirch cedex, France 2 Laboratoire de Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, UPR 9002 du CNRS conventionnée à l'Université Louis Pasteur 15 rue René Descartes, 67084 Strasbourg cedex, France

*To whom correspondence should be addressed. Tel: +33 3 90 24 42 63; Fax: +33 3 90 24 43 12; Email: mely{at}aspirine.u-strasbg.fr

Received October 26, 2004. Revised January 27, 2005. Accepted January 27, 2005.

We report here the synthesis and the spectroscopic characterization of 8-vinyl-deoxyadenosine (8vdA), a new fluorescent analog of deoxyadenosine. 8vdA was found to absorb and emit in the same wavelength range as 2'-deoxyribosyl-2-aminopurine (2AP), the most frequently used fluorescent nucleoside analog. Though the quantum yield of 8vdA is similar to that of 2AP, its molar absorption coefficient is about twice, enabling a more sensitive detection. Moreover, the fluorescence of 8vdA was found to be sensitive to temperature and solvent but not to pH (around neutrality) or coupling to phosphate groups. Though 8vdA is base sensitive and susceptible to depurination, the corresponding phosphoramidite was successfully prepared and incorporated in oligonucleotides of the type d(CGT TTT XNX TTT TGC) where N = 8vdA and X = A, T or C. The 8vdA-labeled oligonucleotides gave more stable duplexes than the corresponding 2AP-labeled sequences when X = A or T, indicating that 8vdA is less perturbing than 2AP and probably adopts an anti conformation to preserve the Watson–Crick H-bonding. In addition, the quantum yield of 8vdA is significantly higher than 2AP in all tested oligonucleotides in both their single strand and duplex states. The steady-state and time-resolved fluorescence parameters of 8vdA and 2AP were found to depend similarly on the nature of their flanking residues and on base pairing, suggesting that their photophysics are governed by similar mechanisms. Taken together, our data suggest that 8vdA is a non perturbing nucleoside analog that may be used with improved sensitivity for the same applications as 2AP.

Correspondence may also be addressed to Alain Burger. Tel: +33 4 92 07 61 53; Fax: +33 4 92 07 61 51; Email: burger{at}unice.fr

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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