Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT and GC hairpin duplex DNA

Insights into binding efficacy and thermodynamic aspects of small molecules are important for rational drug designing and development. Here, the interaction of Harmane (Har), a very important bioactive indole alkaloid, with AT and GC hairpin duplex-DNAs has been reported using various biophysical tools. Detailed molecular mechanism with special emphasis on binding nature, base specificity, and thermodynamics have been elucidated via probing nucleic acids with varying base compositions. Har bound to both the DNA strands exhibited hypochromic effect in absorbance whereas bathochromic and hypochromic effects in fluorescence spectra. The binding constants estimated were in the order of 10(5) M-1 (higher for GC sequence compared with AT) with 1:1 stoichiometry. Noncooperative binding mode has been observed via intercalation in both the cases. The thermodynamic profile was obtained from temperature-dependent fluorescence experiments. Both Har-AT and Har-GC complexations were exothermic in nature associated with positive entropy and negative enthalpy changes. Salt-dependent studies revealed that the binding interaction was governed by nonpolyelectrolytic and hydrophobic interaction forces. The ligand-induced structural perturbation of the DNA structures was evident from the circular dichroism data. Molecular modelling data indicated towards the involvement of hydrophobic forces and hydrogen bonding.

Automated summary

Insights into the binding efficacy and thermodynamic aspects of the interaction between Harmane and AT and GC hairpin duplex-DNAs have been obtained in this study. The binding constants indicate a specific and noncooperative intercalation binding mode. Thermodynamic analysis reveals an exothermic binding process with positive entropy and negative enthalpy changes. Salt-dependent studies suggest the involvement of nonpolyelectrolytic and hydrophobic forces. Ligand-induced structural perturbation of DNA structures has been observed.