Dacarbazine as a minor groove binder of DNA: Spectroscopic, biophysical and molecular docking studies

A detailed investigation on the mode of action and binding mechanism of a potent anticancer drug, 5-(3,3-dimethyl-1-triazeno)-imidazole-4-carboxamide (DCR) with calf thymus DNA (ctDNA) was carried out. UV-vis and fluorescence spectrophotometry suggested the formation of complex between DCR and ctDNA. The binding constant (Kb) determined by ITC was 7.89 × 104 M−1. Thermodynamic parameters obtained by isothermal calorimetry suggested the spontaneous free energy (ΔG < 0) and large favorable enthalpy driven (ΔH < 0) reaction, indicating the key role of hydrogen bonding and van der Waals forces in groove binding process. Moreover, DNA-melting and circular dichroism as well as competitive displacement studies with ethidium bromide, Hoechst 33258 and potassium iodide, clearly established the formation of a groove binding system between the DCR and ctDNA. Molecular docking analysis further confirmed DCR to be a minor groove binder involving hydrogen bonding mediated 'A-T'-rich region of 'B-DNA'.