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 and CD spectroscopy at neutral and acidic pH, in which poly(rA) exists as 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 dye and the negatively charged phosphate groups. The binding constant for the single strand-MB complex decreased from 1.15 x 10(5) M-1 to 7.62 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 neutral 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 intercalation between the adenine bases is also indicated. A red shift in the visible 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.