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

Abstract

The studies on the interaction of intercalators methylene blue (MB) and ethidium bromide (EtBr) with synthetic single-stranded (ss-) polynucleotides poly(rA) and poly(rU) as well as with the formed doublestranded (ds-) poly(rA)-poly(rU), resulted from their hybridization, have been carried out at the ionic strength at the solution of 0.04 mol, in interval of r = phosphate/ligand ratio 0 £ r £ 10. The absorption spectra of the complexes of these ligands with the mentioned polynucleotides were obtained and on the basis of changes of these absorption spectra the binding isotherms in Scatchard’s coordinates were constructed. It was revealed that MB interacts with both poly(rA) and ds-poly(rA)-poly(rU) cooperatively, while in the case of poly(rU), cooperativity is not found out. Coopeartivity is absent at the interaction of EtBr with ssand ds-polynucleotides as well. From the adsorption isotherms, the binding parameters of these ligands with the mentioned polynucleotides – values of association constant K and number of base pairs per binding site n, as well as cooperativity factor value at the interaction of MB with poly(rA) and ds-poly(rA)-poly(rU) were determined. Both ligands were revealed to bind to polynucleotides at least by two modes, though, MB shows much higher affinity to poly(rA), while EtBr – to ds-poly(rA)-poly(rU).