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Nucleic Acids Research 2006 34(5):e43; doi:10.1093/nar/gkl011
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Published online 17 March 2006

Nucleic Acids Research, 2006, Vol. 34, No. 5 e43
© The Author 2006. 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@oxfordjournals.org

Methods Online

BENA435, a new cell-permeant photoactivated green fluorescent DNA probe

Alexandra Erve, Yasmina Saoudi, Sylvie Thirot1, Corinne Guetta-Landras1, Jean-Claude Florent1, Chi-Hung Nguyen1, David S. Grierson1 and Andrei V. Popov*

Inserm, U366, DRDC/CS CEA-Grenoble, 17, rue des Martyrs, F-38054, Grenoble, cedex 9 France 1 Laboratoire de Pharmacochimie, UMR176 CNRS-Institut Curie, Institut Curie Section de Recherche Batiment 110, Centre Universitaire, 91405 Orsay, France

*To whom correspondence should be addressed. Tel: +33 4 38 78 54 82; Fax: +33 4 38 78 50 57; Email: andrei.popov{at}cea.fr

Received October 12, 2005. Revised January 27, 2006. Accepted February 12, 2006.

N'-(2,8-Dimethoxy-12-methyl-dibenzo [c,h] [1,5] naphthyridin-6-yl)-N,N-dimethyl-propane-1,3-diamine (BENA435) is a new cell-membrane permeant DNA dye with absorption/emission maxima in complex with DNA at 435 and 484 nm. This new reagent is unrelated to known DNA dyes, and shows a distinct preference to bind double-stranded DNA over RNA. Hydrodynamic studies suggest that BENA435 intercalates between the opposite DNA strands. BENA435 fluoresces much stronger when bound to dA/dT rather than dG/dC homopolymers. We evaluated 14 related dibenzonaphthyridine derivatives and found BENA435 to be superior in its in vivo DNA-binding properties. Molecular modelling was used to develop a model of BENA435 intercalation between base pairs of a DNA helix. BENA435 fluorescence in the nuclei of cells increases upon illumination, suggesting photoactivation. BENA435 represents thus the first known cell-permeant photoactivated DNA-binding dye.

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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