title: Elucidation of the DNA binding specificity of the natural plant alkaloid chelerythrine: a biophysical approach.
abstract: Interaction of the anticancer plant alkaloid chelerythrine with four sequence specific synthetic polynucleotides was studied by spectroscopy and calorimetry experiments. The binding resulted in strong hypochromic and bathochromic effects in the absorption spectrum of the alkaloid, enhancement in the fluorescence with the AT polynucleotides and the homo-GC polynucleotide and quenching with the hetero-GC polynucleotide. Cooperative binding was observed with all the polynucleotides. Fluorescence polarization anisotropy, iodide quenching and viscosity results confirmed intercalative binding of the alkaloid. The binding resulted in the thermal stabilization of the polynucleotides and moderate perturbations in the B-conformation of the DNA. The high binding affinity values (∼10(6) M(-1)) evaluated from the spectroscopic data was in excellent agreement with those obtained from calorimetry. The binding was exothermic and favoured by negative standard molar enthalpy and positive standard molar entropic contributions in all cases other than homo-AT polynucleotide, where it was endothermic and entropy driven. Salt-dependent calorimetry data revealed that the binding reaction was driven mostly by non-polyelectrolytic forces. The magnitude of the negative heat capacity values confirmed the role of significant hydrophobic effects in the interaction profile of the alkaloid with the polynucleotides. The results revealed the specificity of chelerythrine to follow homo-GC>hetero-GC>hetero-AT=homo-AT polynucleotide.
authors.affiliation: Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India.
authors.forename: Pritha
authors.initials: P
authors.lastname: Basu
authors.affiliation: Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India. Electronic address: gsk.iicb@gmail.com.
authors.forename: Gopinatha
authors.initials: G
authors.lastname: Suresh Kumar
mesh_terms: D000470:Alkaloids / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D053119:Benzophenanthridines / Q000737:chemistry* / Q000378:metabolism; D002151:Calorimetry; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D005454:Fluorescence Polarization; D031541:Fluorescence Resonance Energy Transfer; D009690:Nucleic Acid Conformation; D044367:Phase Transition; D013816:Thermodynamics; D014783:Viscosity
chemical_list: D000470:Alkaloids; D053119:Benzophenanthridines; D004247:DNA; C016299:chelerythrine
keywords: Benzophenanthridine alkaloid; Polynucleotides; Specificity; Thermodynamics