A new 1,4,7-triazacyclononane derivative, 4-benzyloxy-benzyl-1,4,7-triazacyclononane (btacn), and three associated cyclen complexes, Cu(btacn)Cl2, Zn(btacn)Cl2 and [Cu(btacn)2]·(ClO4)2, were prepared to serve as DNA synthesis interferents. The compounds were characterized using IR, 1H and 13C NMR, ESI-MS, elemental analysis and X-ray single crystal diffraction methods, and their DNA damage mechanisms and cytotoxicities towards cancer and normal cells were studied. Among them, Cu(btacn)Cl2 and [Cu(btacn)2]·(ClO4)2 exhibit potent anti-proliferation activity in HepG-2 and HeLa cells, but low cytotoxicity in the normal cell models LO2 and HUVEC, giving SI values (IC50 ratios) ranging from 2.45 to 7.09-times higher than that of cisplatin. DNA binding and cleavage studies suggested that [Cu(btacn)2]·(ClO4)2 can more easily intercalate into CT-DNA than Cu(btacn)Cl2, which is consistent with the results of G2/S phase arrest and apoptosis in HepG-2 cells involving the complexes. In contrast, Zn(btacn)Cl2 demonstrated weak DNA binding and no obvious cytotoxicity. The results suggest that Cu(btacn)Cl2 and [Cu(btacn)2]·(ClO4)2 mainly undergo redox processes to produce reactive oxygen species (ROS) that induce DNA degradation and mitochondrial damage.