Binding of alkaloid harmalol to DNA: photophysical and calorimetric approach

Harmalol exhibits pH dependent structural equilibrium between protonated and deprotonated forms with a pKa of 7.8 as revealed from spectroscopic titration. The compound exists as protonated (structure I) and deprotonated (structure II) form in the pH range 1-7 and 9-12, respectively. The interaction of structure I and II to calf thymus DNA has been studied by different spectroscopic and calorimetric techniques in buffer of pH 6.8 and 9.2, respectively. The results show that structure I bind strongly to DNA showing a cooperative mode with a binding constant of 4.5×10(5)M(-1) and a stoichiometry of 4.8 nucleotide phosphates. The alkaloid stabilized the DNA by 8°C, the binding shows 40% quenching of fluorescence intensity, perturbation in circular dichroism spectra and enthalpy driven exothermic binding with a large hydrophobic contribution to the binding free energy. Furthermore, the alkaloid shows a prominent change of specific viscosity with sonicated linear DNA and unwinding-rewinding of covalently closed pUC 18 DNA, revealing intercalative binding. The deprotonated structure (structure II), on the other hand, in the presence of large amount of DNA concentration, converts back to a structure I-DNA complexation. This transition has been presumably induced by the polyanionic phosphate backbone of DNA at high concentration.