Photophysical and thermodynamic delineation of binding interactions of anticancer alkaloid chelerythrine towards triplex and duplex DNA structures: a comparative approach

Abstract

Higher-order nucleic acid structures have garnered attention nowadays in the field of active cancer research owing to their wide range of applications in gene regulation and targeted gene therapy. Chelerythrine (CHL), a benzophenanthridine plant alkaloid, exhibits important biological activities and has therapeutic applications. In this article, we endeavour to elucidate the comparative binding interactions of chelerythrine (CHL) with the triplex (T.A*T) and duplex (A.T) structures of DNA by performing a series of spectroscopic studies and theoretical calculations. UV-visible absorption spectrophotometric studies and spectrofluorimetric studies showed stronger binding affinity of CHL towards T.A*T compared with its parent duplex form, i.e. A.T. Thermal melting experiments revealed a substantial thermal stabilization of the Hoogsteen base-paired strand of the T.A*T triplex (up to ∼31.4 °C), while the Watson–Crick base-paired strands of both triplex and duplex forms were moderately stabilized (up to ∼9 °C). Fluorescence quenching studies, steady-state anisotropy studies, competitive displacement assays, and circular dichroism studies confirmed an intercalative binding mode in both cases, and the extent of intercalation was found to be stronger in the case of the triplex compared with the parent duplex form. Fluorescence lifetime measurements and time-resolved anisotropy decay studies demonstrated significant alteration in the excited-state behaviour and rotational dynamics of CHL within the DNA triplex- and duplex-bound environments, respectively. Analysis of the thermodynamic parameters revealed that the complexation of CHL with both forms of DNA helices was characterized by negative enthalpy changes and negative entropy changes. Theoretical calculations using DFT and TD-DFT methods validated the experimental optical spectroscopic behaviour of the ligand CHL, as obtained from both absorption and fluorescence studies. Elucidation of such structural and energetic facets involved in the association of CHL with the DNA triplex and duplex forms may offer new scope for strategic nucleic acid-targeted drug design.