Spectroscopic, electrochemical and molecular docking study of the binding interaction of a small molecule 5H-naptho[2,1-f][1,2] oxathieaphine 2,2-dioxide with calf thymus DNA

The interaction of 5H-naptho[2,1-f][1,2]oxathieaphine2,2-dioxide (NOTD) with calf thymus DNA in Tris-HCl buffer at physiological pH was investigated with the help of various spectroscopic and electrochemical methods along with molecular docking study. Studying the non-covalent binding interaction of a neutral fluorophore with ctDNA has become an active field of research at the interface between medicinal chemistry and biological science. NOTD is known for its various toxicological, skin sensitization, and antiviral properties. Still, to date, its interaction style with ctDNA is not well elucidated. UV-vis absorption, fluorescence emission and circular dichroism spectroscopy (CD) suggest the complex formation between NOTD and ctDNA with binding constant value in the order of 3.12-4.1( × 104) M−1. Binding nature of NOTD with ctDNA is affirmed from the DNA helix melting experiment, comparative displacement assay using known DNA intercalator, cyclic voltammetry and finally molecular docking study. It was evident from experimental result that the probe NOTD binds with ctDNA in groove binding mode as manifested by a decrease in iodide quenching effect, spectral change in CD, a substantial increase in denaturing temperature in DNA and change in potential value. Furthermore, the molecular docking study insisted the above mentioned experimental result in a very affectionate way.

represent the groove binding of NOTD with calf thymus DNA143