DNA minor groove binding of small molecules: Experimental and computational evidence

Abstract

Eight indole derivatives were studied for their DNA binding ability using fluorescence quenching and molecular docking methods. These indole compounds have structural moieties similar as in few indole alkaloids. Experimental and theoretical studies have suggested that indole derivatives bind in the minor groove of DNA. Thermodynamic profiles of DNA complexes of indole derivatives were obtained from computational methods. The complexes were largely stabilized by H-bonding and van der Waal’s forces with positive entropy values. Indole derivatives were found to possess some Purine (Pu) — Pyrimidine (Py) specificity with DNA sequences. The results obtained from experimental and computational methods showed good agreement with each other, supported by their correlation constant values.