A molecular biophysics study of interaction between berberine and ct-DNA in absence and presence of linker histone

Small molecules by binding to the histone-DNA complex, interfere with important cellular processes such as cell division and growth in cancerous cells, resulting in apoptosis. The study of the interaction of small molecules with histone-DNA complex is important for better understanding their mechanism of action and to design newer and more effective drug compounds. This treatise, the interaction of Berberine chloride (Ber) with a histone-DNA complex was investigated using different spectroscopic and molecular modeling techniques. Fluorecense quenching of ct-DNA upon interaction with Ber determine the binding of Ber to ct-DNA with Ksv = 9.46×107 M-1. Ksv value of ct-DNA-Ber in the presence of H1 is 3.10×107 M-1 that show the H1 caused the reduction of binding affinity of Ber to ct-DNA. The ΔH0 and ΔS0 values of ct-DNA-Ber complex formation in absence and presence of H1 determine two different behaviors in binary and ternary systems from the view point of interaction forces. In competitive emission spectrum, ethidium bromide (EB) and acridine orange (AO) as intercalator probes , by adding up Ber to ct-DNA complexes, ctDNA-EB and ctDNA-AO, the change in the emission spectra showed competition, but in the presence of histone H1, competition between ligands and probes was not observed. Melting temperature (Tm) curve results, show that the binding mode of Ber to ctDNA in absence and presence of H1 were intercalative and groove binding respectively. The viscosity results confirm the different behavior of interaction between ctDNA and Ber in binary and ternary systems.

Keywords:

DNA Interaction , Berberine chloride , Spectroscopy , UV-Visible , Ct-DNA , Intercalation , Groove binding , Linker Histone