Copper(II) complexes are known to play a significant role in both naturally occurring biological systems and pharmaceutical agents. Recently, Cu(II) complexes have gained importance in DNA cleavage essential for the development of anticancer drugs and chemotherapeutic agents. Therefore, we have designed small molecules, consisting of a metal ion, N,N-donor ligands, and dipeptides, to probe their DNA-cleaving potential. Accordingly, the interaction of Cu(II) with ethylenediamine, histamine and the dipeptides histidylglycine, histidylalanine, and histidylleucine has been investigated. The binding modes, stabilities, and geometries of these complexes were determined by various physicochemical techniques. Their DNA-binding abilities were probed by absorption and fluorescence spectroscopy, and their DNA-cleavage potential was tested by electrophoresis.