Binding behaviour of aminoglycoside drug kanamycin with calf thymus DNA: Thermodynamic, spectroscopic and molecular modelling studies

In this work, the binding mode of antibiotic drug kanamycin with Calf thymus DNA (ctDNA) was assessed using thermodynamic, spectroscopic and molecular docking studies. Isothermal Titration Calorimetry (ITC) studies suggest that the binding is enthalpically favored with a small entropic change and a binding constant of the order of 104 mol−1 dm3, which remains almost same in the studied temperature range. Studies in the presence of osmolytes tetraethylene glycol and sucrose show no appreciable change in the binding behaviour as well as on the stability of the DNA-kanamycin complex. These finding suggests that the number of water molecule released or taken up is not significant in the binding process. Competitive fluorescence displacement assay and circular dichroism studies show that kanamycin follows groove binding mode of interaction. Molecular docking studies also supports that kanamycin prefers groove binding mode, stabilized by hydrogen bonding.