Peculiarities of interaction of synthetic polyribonucleotide poly(rA)-poly(rU) with some intercalators

Study of complexation of single-stranded poly(rA) and poly(rU) with methylene blue

To reveal the effect of DNA- or RNA-specific low-molecular compounds on cellular processes on the molecular level, we have carried out the studies with the application of spectroscopic methods. It is necessary for the understanding of structural-functional properties of nucleic acids in cell. In this work the interaction of DNA-specific thiazine dye methylene blue (MB) with synthetic polynucleotides poly(rA) and poly(rU) was studied. The interaction of MB with synthetic polyribonucleotides poly(rA) and poly(rU) was examined in the solution with high ionic strength in a wide phosphate-to-dye (P/D) range, using the absorption and fluorescence spectroscopies, as well as the fluorescence 2D spectra and 3D spectra analyses were given. Values of the fluorescence quenching constants for the complexes of MB with poly(rA) and poly(rU) were calculated (KSV is the Stern-Volmer quenching constant). Two different modes of MB binding to single-stranded (ss-) poly(rA) and poly(rU) and to their hybrid double-stranded (ds-) structure - poly(rA)-poly(rU) were identified. This ligand binds to ss-poly(rA) and poly(rA)-poly(rU) by semi-intercalation and electrostatic modes, but to ss-poly(rU) the prevailing mode is the electrostatic interaction.Communicated by Ramaswamy H. Sarma.

Hybridization kinetics of DNA fragments in the presence of ligands intercalating into DNA-duplexes

In this work the hybridization kinetics of DNA fragments on underlayer has been studied, when besides single-stranded DNA molecules there are also ligands in the medium that are able to intercalate into DNA-duplexes. A system of differential equations was obtained that describes the correlative change of the number of DNA-duplexes on the underlayer and the change of the number of ligands intercalating into DNA-duplexes. It was shown that the rate of underlayer filling by DNA-duplexes increases along with the enhancement of both equilibrium constant of formation reaction of DNA-duplexes and the concentration of DNA targets in the solution. It was also shown that the intercalation kinetics of ligands into DNA-duplexes relevantly depends on relation of dissociation rate constant of DNA-duplex to dissociation rate of the ligand complex with DNA-duplex.Communicated by Ramaswamy H. Sarma.

Study of the influence of the ionic strength on complex-formation of ethidium bromide with poly(rA)-poly(rU)

Communicated by Ramaswamy H. Sarma.