SPECTROSCOPIC STUDIES ON THE BINDING OF METHYLENE-BLUE TO POLY(RIBOADENYLIC ACID)

The binding of methylene blue (MB) to poly(rA) was studied using UV an d CD spectroscopy at neutral and acidic pH, in which poly(rA) exists a s a single strand and a duplex respectively. UV spectroscopic studies and analysis of equilibrium binding data show that salt increases the cooperativity parameter but reduces the binding between the cationic d ye and the negatively charged phosphate groups. The binding constant f or the single strand-MB complex decreased from 1.15 X 10(5) M-1 to 7.6 2 X 10(3) M-1 while the cooperativity parameter increased from 9 to 71 , when salt concentration was increased from 1 mM to 200 mM. At neutra l pH, changes in the induced circular dichroism of MB-poly(rA) complex with ionic strength show predominance of electrostatic binding to the phosphate group externally on the poly(rA) chain, a partial intercala tion between the adenine bases is also indicated. A red shift in the v isible absorption band and the ICD profile of the double stranded poly (rA)-MB complex suggest an electronically coupled intercalation mode for the dye binding at pH 4.2.