Fisetin (FTN) and its metal chelates are critically important since this bioflavonoid possesses wide range of pharmacological properties. Usually, metal binding property enhances the pharmaceutical activity of FTN. Thus in this report, we investigated the complexation of FTN with biologically essential metal ion Cu(2+) and further examined the effect of such complexation on calf thymus DNA (CT DNA) binding in comparison with free FTN. We have characterized the complex formation of FTN with Cu(2+) using UV-visible, fluorimetric and FTIR studies. Within our experimental concentration range we found that, FTN forms a 2:1 complex with Cu(2+) in terms of FTN:Cu(2+). Spectroscopic analysis revealed that both FTN and FTN(2)-Cu(2+) complex bind with CT DNA and the binding constant is higher for free FTN. Perturbation of circular dichroism spectrum of CT DNA was observed in presence of free FTN due to structural alteration in DNA double helix. Viscometric, thermal melting and fluorescence quenching study confirm that FTN intercalates in between the base pairs of CT DNA while its Cu (II) complex acts as a groove binder. Molecular docking study further confirms that FTN intercalates into AT rich region of CT DNA while its Cu (II) complex binds at the minor groove.