Polymorphic RNA-Templated Modulation of Photophysics and Dynamics of a Molecular Rotor with Contrasting Affinity: A...

Photophysical studies on the interaction of small molecules with various forms of nucleic acids are attracting attention nowadays in order to delineate the molecular level mechanism of various biological processes occurring in vivo. Herein, we employed vivid steady-state and time-resolved spectroscopic techniques to elucidate the detailed characterization of the binding interaction of a biologically active cationic dye thioflavin T (ThT) with double and triple helical forms of RNA - A.U duplex and U.A*U triplex respectively. In both the cases, binding was accompanied by bathochromic and hypochromic shifts of absorption maxima of ThT along with significant regaining of fluorescence intensity which was intrinsically lost due to rapid transition from a locally excited state to nonradiative twisted intramolecular charge-transfer state through torsional rotation of BZT and DMAB rings around the C-C single bond. The binding constant was found to be greater with U.A*U triplex (K_b ∼ 10⁵ M^-1) than A.U duplex (K_b ∼ 10⁴ M^-1) at 293.15 K. However, steady-state absorption study, steady-state and time-resolved spectrofluorimetric and anisotropic study, anionic quenching study, circular dichroism study, and fluorescence contact energy-transfer analysis unveiled that the binding mode was partial intercalation in both the cases and the extent of intercalation was stronger in A.U duplex. Apparent anomaly in the binding affinity and intercalation strength probably lies in the interplay of two factors, namely, nonplanar structure of ThT and Columbic relaxation on binding. In both the cases, the binding was driven by a negative enthalpy change and a positive entropy change, and the van der Waals interaction together with H-bonding interactions are the major governing forces underlying the complexation. We also observed that the systematic addition of orange-emitting ethidium bromide to cyan-emitting ThT-RNA complex led to bright white light emission through Forster-type resonance energy-transfer mechanism, and this energy transfer was more feasible in the interstrand condition. This work renders the utility of ThT as a potential prerequisite for its application in pharmacological and optoelectronics industries.