Biopolym. Cell. 1999; 15(1):75-82.
http://dx.doi.org/10.7124/bc.000509
Methods
Interaction of cyanine dyes with nucleic acids. 5. Towards model of «half intercalation of monomethyne cyanine dyes into double-stranded nucleic acids
1Yarmoluk S. M., 1Kovalska V. B., 2Kovtun Yu. P.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Institute of organic chemistry NAS of Ukraine
    5, Murmanska Str., Kyiv, Ukraine, 02660

Abstract

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 nucleophilic groove whereat 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 series of structure-like 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. Monomethyne pyria'inium cyanine dye (Cyan 40; 4-((1-methyl-benzothiazoleilidene-2)methyl: 1,2,6-trimethylpyridinium p-toluenesulfonatc 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.
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