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Synthesis of new complexes of 1-(o/p-carboxy phenyl)-4, 4, 6-trimethyl pyrimidine-2-thione (o/p-HCPPT) with metals (M(II) = Cu, Mn, Ni, Co, Zn, Pd ), taking Cu and Ni metals common to both ortho and para ligands for comparison and evaluation of their biological potential. The antibacterial activity of synthesized metal complexes [M(o/p-CPPT)2] was evaluated by microdilution method using DMSO as a solvent against non-pathogenic bacterial strain of E.coli MTCC 9537. All the synthesized complexes were evaluated for their DNA nicking activity. These metal complexes were characterized by 1H-NMR, FTIR, UV–Vis, ESI-mass spectrometry, molar conductivity, magnetic moment measurements. 1H-NMR and IR results showed that coordination occurs via N and S forming four-membered cyclic ring. Mass spectrum and Elemental analysis showed the formation of 1:2 metals to ligand stoichiometry. Ligand with para substitution and its complexes with Cu(II) and Ni(II) metal exhibited very good DNA photocleavage activities as compared to the ligand with ortho substitution and its metal complexes.