Thermodynamics of the Interaction of Synthetic Polynucleotide Poly(rA)-Poly(rU) with Intercalators

Abstract

The melting of poly(rA)-poly(rU) and its complexes with the intercalators — methylene blue (MB) and ethidium bromide (EtBr) has been carried out at the ionic strength of the solution 0.02, 0.04, and 0.1 M. It was revealed that this polynucleotide has the non-stable double-stranded structure at the ionic strength of 0.02 M and it becomes more stable at the complex-formation with the mentioned ligands. The increase of the solution ionic strength also results in the stabilization of the double-stranded structure of the polynucleotide, in consequence of which the interaction of the MB and EtBr with the poly(rA)-poly(rU) becomes more preferable and more beneficial thermodynamically. It was shown that at the ionic strength of 0.1 M the poly(rA)-poly(rU) takes a structure that is more available to the intercalation of both ligands. In the case of the MB the main binding mode becomes a semi-intercalation, while in the case of the EtBr all the intrinsic binding modes are displayed. It was also shown that in the case of the EtBr the values of ΔH and ΔS increase, while in the case of the MB, ΔH and ΔS those values increase, then decrease at the enhancement of the ionic strength of the solution.