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 (K-SV 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

Automated summary

To understand the effect of DNA- or RNA-specific low-molecular compounds on cellular processes at the molecular level, spectroscopic methods were used in this study. The interaction between the DNA-specific thiazine dye methylene blue (MB) and synthetic polynucleotides poly(rA) and poly(rU) was investigated. The results showed different binding modes of MB to single-stranded and double-stranded structures of the polynucleotides. This study contributes to the understanding of the structural-functional properties of nucleic acids in cells.