Biochemically active Cu(II) and Zn(II) complexes [CuL(ClO4)2(1) and ZnL(ClO4)2(2)] have been synthesized from N,N donor Schiff base ligand L derived from4,6-dichloropyrimdine-5-carboxaldehyde with 4-(2-aminoethyl)morpholine. The L, complexes 1 and 2 have been structurally characterized by elemental analysis, 1H-NMR, FTIR, MS, UV-Visible and ESR techniques. The results obtained from the spectral studies supports the complexes 1 and 2 are coordinated with L through square planar geometry. DFT calculations results supports, the ligand to metal charge transfer mechanism can occur between L and metal(II) ions. The antimicrobial efficacy results have been recommended that, complexes 1 and 2 are good anti-pathogenic agents than ligand L. The interaction of complexes 1 and 2 with calf thymus (CT) DNA has been studied by electronic absorption, viscometric, fluorometric and cyclic voltammetric measurements. The calculated Kb values for L, complexes 1 and 2 found from absorption titrations was 4.45 × 104, L; 1.92 × 105, 1 and 1.65 × 105, 2. The Ksv values were found to be 3.0 × 103, 3.68 × 103and 3.52 × 103 for L, complexes 1 and 2 by using competitive binding with ethidium bromide (EB). These results suggest that, the compounds are interacted with DNA may be electrostatic binding. The molecular docking studies have been carried out to confirm the interaction of compounds with DNA. Consequently, in vitro anticancer activities of L, complexes 1 and 2 against selected cancer (lung cancer A549, liver cancer HepG2 and cervical carcinoma HeLa) and normal (NHDF) cell lines were assessed by MTT assay. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.