Molecular Spectroscopy and Molecular Dynamic Simulation to Study the Binding of DNA with 3-Hydroxy-2-oxindole

This study aimed to investigate the interaction between 5-(2-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl)-1,3thiazolidine-2,4-dione (oxindole A) and DNA with and without ultrasound treatment. Absorption studies have indicated that oxindole A could bind to CT-DNA with the binding constant of 30,000 and 26,666 M-1 with and without ultrasound treatment, respectively. In the competitive fluorescence method, the displacement of 4′,6-diamidino-2-phenylindole (DAPI) as a probe bound to the groove, from the DNA groove occurred by oxindole A. Using the Stern-Volmer plot, quenching constant was calculated to be 1,411 and 2,753 M-1 with and without ultrasound, respectively. Viscometric experiments have confirmed the groove binding of oxindole A to the DNA, which is consistent with the molecular dynamic simulation. The analysis of Pi, as a measure of affinity for ligand binding, has also revealed that the DA3, DG4, DC5, DT7, DC8, and DG9 of DNA have the highest affinity toward oxindole A. In addition, the results of the cell viability assay of the DU145 cell line have demonstrated that oxindole A has cytotoxic effects.