Evidence for Dual Site Binding of Nile Blue A toward DNA: Spectroscopic, Thermodynamic, and Molecular Modeling Studies

Abstract

Binding of Nile Blue (NB) with calf thymus DNA has been studied using molecular modeling, spectroscopic, and thermodynamic techniques. Our study revealed that NB binds to the DNA helix by two types of modes (groove binding and intercalation) simultaneously. The thermodynamic study showed that the overall binding free energy is a combination of several negative and positive free energy changes. The binding was favored by negative enthalpy and positive entropy changes (due to the release of water from the DNA helix). The docking study validated all experimental evidence and showed that NB binds to a DNA minor groove at low concentrations and switches to intercalation mode at higher concentrations.