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

• Rhodamine B changes the conformation of DNA during the binding process.
• The binding process is cooperative initially but become non-cooperative later.
• Rhodamine B binds in the minor groove of DNA.
• The binding is favored by both negative enthalpy change and positive entropy change.
• The binding has both salt dependent and salt independent potential.

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 103 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.

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