A complex formulized as [Cu(dmpn)2(OH2)][Cu2(DPA)4μ-Cu(dmpn)2].H2O (1), where dmpn is 2,2′-dimethyl- 1,3-diaminepropane and DPA is dipicolinic acid (H2dipic), was synthesized and characterized by X-ray crystallography, conductivity measurement, thermogravimetric (TG) analysis, spectroscopic methods (IR, Mass, UV–Vis, EPR). Magnetic properties of complex (1) were studied at room temperature with vibrating sample magnetometer (VSM). The results indicated that the complex exhibits paramagnetic behavior. The initial in vitro cytotoxic activity of complex (1) showed promising results against HCT116 colon cell lines compared to the known anticancer drugs such as cisplatin. In the recent study, the mode of interaction between DNA and complex (1) was explored using different techniques. The experiments revealed that the mechanism of fluorescence quenching is static and the characteristic of this interaction is exothermic. The apparent binding constant (Kapp = 1.9 × 103 M 1) shows that the interaction between the Cu(II) complex and DNA is probably non-intercalation. Based on other data, it can be suggested that hydrogen bonding, and van der Waals forces play a major role in this interaction. Molecular docking simulation supported the achieved experimental results. Likewise, complex (1) shows nuclease activity in the presence of H2O2 and can cleavage the structure of DNA.