Novel copper(II) complexes bearing 2,2′-bipyridine (bpy) derivatives with adenine, thymine and uracil nucleobases [Cu(L1)Cl2]·2H2O (1), [Cu(L2)Cl2] (2) and [Cu(L3)Cl2]·H2O (3) (L1 = 5,5′-Di[N9-adenylmethyl]-2,2′-bipyridine, L2 = 5,5′-Di[N1-thyminylmethyl]-2,2′-bipyridine and L3 = 5,5′-Di[N1-uracilmethyl]-2,2′-bipyridine) were synthesized and characterized. Structure simulation was performed for these complexes. Circular dichroism (CD) spectra revealed the interactions between these ligands and pBR322 DNA and showed that the local DNA structure was perturbed by these ligands. Cleavage of pBR322 DNA by these complexes was carried out in 20 mM HEPES (pH 7.5) at 37 °C. The calculated pseudo-Michaelis–Menten kinetic parameters (kcat) were 14.7 ± 0.6 and 40.4 ± 1.3 h−1 for 1 and 2. The cleavage efficiency of 2 was 80-fold higher than that of its simple analogue [Cu(bpy)Cl2] (kcat = 0.50 h−1) and very close to the catalytic rate constant of natural EcoRI endonuclease (kcat = 43.2 h−1) at similar conditions. Thus, complex 2 might be one of the most effective artificial nucleases that could catalyze double-stranded DNA hydrolytic cleavage so far. Hydrolytic mechanisms involved in DNA cleavage were explored using radical scavengers and T4 ligase. Competitive experiments with special binding agents showed that complexes 1–3 could preferentially bind to the minor groove of double-stranded DNA, suggesting specific DNA binding characteristics. Molecular docking calculations also indicated that complexes 1–3 could bind to the minor groove of targeted DNA much more strongly than their simple analogues and preferentially bind at the AT region of the dodecamer. Such high DNA cleavage ability and selectivity of these copper(II) complexes could be attributed to the synergic effects of the metal center and the pendant nucleobases.
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