Affinity Assessment of DNA-Specific of Ethidium Bromide and Methylene Blue Intercalator Ligands with Poly(rA), Poly(rU), and Poly(rA)-Poly(rU)

The interaction of methylene blue (MB) and ethidium bromide (EB) intercalators with synthetic single-strand (ss) polynucleotides poly(rA) and poly(rU) and the double-strand (ds) poly(rA)-poly(rU) formed as a result of their hybridization was investigated in 0.04 mole solution in the range of phosphate/ligand ratios r = 0 <= r <= 10. The absorption spectra of complexes of the ligands with the polynucleotides were obtained, and adsorption isotherms in Scatchard coordinates were constructed on the basis of changes in the absorption spectra. It was found that MB interacts cooperatively with poly(rA) and also with ds-poly(rA)-poly(rU), while cooperation is not detected in the case of poly(rU). There is also no cooperation in the interaction of EB with ss- and ds-polynucleotides. The binding parameters for the interaction of these ligands with the polynucleotides (the association constants K and the number of bases n per binding site and also the cooperation factor) in the interaction of MS with poly(rA) and ds-poly(rA)- poly(rU) were determined from the adsorption isotherms. Both ligands were found to bind to polynucleotides by at least two methods, and MB here exhibits much higher affinity to poly(rA) and EB to ds-poly(rA)-poly(rU).