Binding of DNA with Rhodamine B: Spectroscopic and molecular modeling studies

Binding of Rhodamine B to Calf thymus DNA (CT DNA) was studied using various biophysical techniques and molecular docking method. Circular dichroic studies revealed that conformation of CT DNA changed moderately and unwind on binding with Rhodamine B. The binding was cooperative in nature. The overall binding constant, evaluated from Benesi Hidebrand plot was seen to be in the range of 10(3) M-1. Salt dependence binding data showed that the binding free energy depends on salt concentration. From the thermodynamics studies, it was concluded that binding process is favored by both negative enthalpy change and positive entropy change. Molecular docking calculations and Quenching experiment confirmed that the dye binds in the minor groove of CT DNA. These results further advance our knowledge on the molecular aspects on the interaction of these types of dyes to nucleic acids. (C) 2013 Elsevier Ltd. All rights reserved.