A Comparative Study of the Influence of Aquaous 2,2,2-Trifluoroethanol And Ethanol on the Structural Organization, the Kinetic and Thermodynamic Properties of Oligodeoxyribonucleotides Intermolecular Complex Formation

A comparative study of the structural organization, thermodynamic and kinetic properties of the oligodeoxynucleotides complexes formation in the presence of 2,2,2-trifluoroethanol and ethanol in aqueous solution (volume fraction of alcohol 0 to 50 %) was performed. No significant changes in the circular dichroism spectra of oligonucleotides and their complexes at the adding of 50 % v/v alcohol into a solution, was observed, and they retain the profile typical for B-form DNA. The study of the thermal stability of DNA duplexes showed that the increase in the volume fraction of ethanol in the aqueous solution up to 50 % results in a linear decrease in the melting temperature of the intermolecular DNA complexes. In the case of the 2,2,2-trifluoroethanol we observed atypical dependence of thermal stability of DNA duplexes on the fraction of the fluorine-containing co-solvent. Increasing the alcohol fraction from 0 to 20% v/v led to a linear decrease of the melting point of the complex. A further increase in the volume fraction of alcohol (up to 50 %) did not change the thermal stability of the duplexes. It was shown, that the destabilizing effect of the two co-solvents is due to the increase of the dissociation rate constant of the complex and has mainly entropic nature. On the example of oligonucleotides complexes of 8, 12, 15 and 20 base pairs length the possibility of prediction DNA duplexes thermal stability was shown. A model taking into account the change of a number solvent molecules interacting with nucleic acids at the duplex formation in aqueous ethanol (50 % v/v) or trifluoroethanol (20 % v/v) was applied. An accuracy of melting temperature prediction was 1.3 and 0.6 degrees. Using this model, we found that the addition of alcohols in solution leads to an increase in the number of water molecules that bind to a complementary pair of nucleotides at the formation of intermolecular complex (in the presence of ethanol or trifluoroethanol 0.51 ± 0.09 and 1.33 ± 0.12, respectively). At the same time, alcohols interacted with single-stranded oligonucleotides and double-stranded in the same way