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

Alexandra Erve (1) , Yasmina Saoudi (1) , Sylvie Thirot (2) , Corinne Guetta-Landras (2) , Jean-Claude Florent (2) , Chi-Hung Nguyen (2) , David S. Grierson (2) , Andrei V. Popov (1)

1 Organisation Fonctionnelle du Cytosquelette
2 CSVB - Conception, synthèse et vectorisation de biomolécules

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.

Domaines: Biochimie, Biologie Moléculaire

Alexandra Erve, Yasmina Saoudi, Sylvie Thirot, Corinne Guetta-Landras, Jean-Claude Florent, et al.. BENA435, a new cell-permeant photoactivated green fluorescent DNA probe.. Nucleic Acids Research, 2006, 34 (5), pp.e43. ⟨10.1093/nar/gkl011⟩. ⟨inserm-00380059⟩