Binding of the phenothiazinium dye methylene blue with single stranded polyriboadenylic acid

The binding of the phenothiazinium dye methylene blue to single stranded poly(riboadenylic acid) was investigated by spectroscopic and calorimetric techniques. The binding was cooperative and the affinity was of the order of 106 M−1 at 100 mM [Na+] as determined from absorbance, fluorescence and calorimetric studies. Ferrocyanide quenching studies showed intercalative binding of methylene blue to poly(riboadenylic acid). The binding perturbed the circular dichroism spectrum of poly(riboadenylic acid) with concomitant formation of prominent exciton split type of extrinsic CD bands in the 550–700 nm region. The interaction involved a single binding mode with a 1:2 binding stoichiometry. The binding affinity increased with [Na+] ion concentration in the range 10–200 mM [Na+]. Dye binding induced self-assembled duplex formation in poly(riboadenylic acid). The biological utility of the dye methylene blue in probing nucleic acid structure is revealed from these studies.

► The phenothiazinium dye methylene blue binds strongly and cooperatively with poly(riboadenylic acid). ► The binding was enthalpy driven. ► The binding affinity increased in the range of [Na+] ion concentration, 10–200 mM. ► The binding induces self-assembled structure formation in poly(riboadenylic acid).