Interaction of naturally occurring bioactive flavonoids 5,6,7-trihydroxyflavone (Baicalein) and 7,8-dihydroxyflavone (DHF) binding with calf thymus deoxyribose nucleic acid (dsDNA) was studied by employing UV absorption, fluorescence, circular dichroism, cyclic voltammetric and molecular modeling techniques. All studies were confirmed that the structural changes of DNA binding to the flavonoid. From the CV results positive shift in peak potential and increased peak current of the flavonoid in the presence of DNA and then the fluorescence quenching of DNA-flavonoids system indicated the intercalative mode of binding between flavonoid and DNA. CD studies suggest the conformational changes in DNA upon interaction with the flavonoids. Molecular docking simulation methods are used as tools to delineate the binding mode and probable location of the flavonoids and their effects on the stability and conformation of Ct-(ds) DNA. Furthermore, Baicalein can bind with more potential with Ct-(ds) DNA than DHF. This is helpful to understand the molecular aspects of binding mode and provides direction for the use and the design of new effective therapeutic agents. These results could provide useful information for insight into the pharmacological mechanism of flavonoids.