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Vol 48(2014) N 5 p. 741-748; DOI 10.1134/S0026893314050100 Full Text

O.K. Mamaeva1, A.G. Gabrielyan2, G.L. Arutyunyan2, T.N. Bocharova3, E.A. Smirnova3, A.A. Volodin3, A.K. Shchyolkina1, D.N. Kaluzhny1*

Promoting DNA Molecules Association by Amphiphilic Derivatives of 1,3-Diazaadamantanes Containing Hydrophobic Side Chains

1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
2Mndzhoyan Institute of Fine Organic Chemistry, Science and Technology Center for Organic and Pharmaceutical Chemistry, National Academy of Sciences of the Republic of Armenia, Yerevan, 0014 Armenia
3Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182 Russia

*uzny@mail.ru
Received - 2014-04-25; Accepted - 2014-04-28

Earlier, a new class of compounds, amphiphilic derivatives of 1,3-diazaadamantanes, capable of facilitating the strand exchange in the system of short oligonucleotides, has been discovered. Longer hydrophobic side chains in 1,3-diazaadamantanes have been found to promote stronger acceleration of the reaction. In this study, the interaction of two 1,3-diazaadamantane derivatives containing different side chains with DNA was investigated using optical methods. Concentrations of micelle formation by the 1,3-diazaadamantanes, as well as the ranges of concentrations where the compounds/water mixtures exist in the form of true solutions, were determined based on the increase in the fluorescence intensity of 1-anilinonaphthalene-8-sulfonate probe. The affinities of 1,3-diazaadamantanes to DNA were determined with fluorescent intercalator displacement (FID) assay. A significant increase in the hydrodynamic volume of short DNA hairpins in complexes with 1,3-diaz-aadamantanes was revealed by the estimation of the fluorescence polarization of ethidium bromide probe bound in the hairpins. The intermolecular association of DNA hairpins upon binding with 1,3-diazaadamantanes was confirmed by Forster resonance energy transfer in an equimolar mixture of hairpins fluorescently labeled with Cy-3 or Cy5. In the study, the number of positive charges on 1,3-diazaadamantane derivatives that contain side chains of different lengths was demonstrated to affect their affinity to DNA, while longer hydrophobic side chains ensured more efficient interaction between the DNA duplexes that may facilitate DNA strand exchange.

intermolecular DNA interactions, oligonucleotides, 1,3-diazaadamantanes, fluorescence, computer modeling



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