Interaction of cyanine dyes with nucleic acids. 5. Towards model of «half intercalation of monomethyne cyanine dyes into double-stranded nucleic acids

Recently we have proposed a model of «half intercalation» of monomethyne cyanine dye into the double-stranded helix.Benzothiazole terminal heterocycle «classically» intercalates, nestled between the adjacent base pairs just when second heterocycle is spatially fixed by nucleic acid groove.We consider that heterocycle with high basicity hits in the more nucteophilic groove whereas heterocycle with low basicity insert in more electrophilic interbase space.The purpose of this study is to determine the possible fixation mode of second heterocycle in nucleic acid groove.We synthesized and investigated the stries of structure-tike cyanine dyes which have different charge electronic distribution.We suppose that binding of second heterocycle of high basicity is caused by both spatial fixation and electrostatic interaction, with phosphate group of nucleic acid.Mommethyne pyridinium cyanine dye (Cyan 40; 4-[( 1-m.ethylbenzothiazoleilidene-2)methyIJJ,2,6-trimethylpyridiniurn p-toluenesulfonate interacted with native DNA and RNA with strong fluorescence enhancement.It seems to be perspective for the development of new nucleic acid binding cyanine dyes.