Interaction of sanguinarine with A-form and protonated form of ribonucleic acid structures: Spectroscopic, viscometric and thermodynamic studies

The interaction of sanguinarine with the A-form and the protonated form of poly(rG).poly(rC) has been investigated using a combination of spectrophotometric, spectrofluorimetric, circular dichroic (CD), viscometric and thermodynamic studies. The formation of the two forms of this structure has been confirmed from UV-absorption and CD spectral characteristics. The binding of sanguinarine to both the A-form and the protonated form RNA structures is characterized by the typical hypochromic and bathochromic effects in the absorption spectrum, quenching of fluorescence intensity, decrease in fluorescence quantum yield of the alkaloid, an increase in fluorescence polarization anisotropy and perturbation in the CD spectrum. Scatchard plots obtained from spectrophotometric and spectrofluorimetric analyses show that sanguinarine binds to both the structures in a non-cooperative manner. The binding parameters, according to an excluded site model, indicate a relatively high affinity of the alkaloid binding to the A-form structure than to the protonated form structure. Viscometric studies demonstrate that there is no increase in the contour length of the sonicated A-form and the protonated form RNA structures upon binding to sanguinarine. Thermodynamic parameters as revealed from van't Hoff plot indicate that the RNA binding of the alkaloid is an exothermic process and it binds more tightly to the protonated form than the A-form structure. The intermolecular interaction of sanguinarine is characterized by negative enthalpy changes and positive entropy changes at the binding site of the two structures.