Secondary structure specificity of the nuclease activity of the 1,10-phenanthroline-copper complex

Abstract

The artificial DNase activity of the 1,10-phenanthroline-cuprous ion complex [(OP)2Cu+] and H2O2 cleaves the A, B, and Z forms of DNA at different rates. The B structure, formed by most DNAs including poly(dA-dT) and poly(dA) X poly(dT), is the most susceptible to cleavage. It is completely degraded within 1 min by 40 microM 1,10-phenanthroline/4 microM Cu2+/7 mM H2O2/7 mM 3-mercaptopropionic acid. The A structure, formed by RNA X DNA hybrids such as poly(rA) X poly(dT), is cleaved in both strands roughly 10-20% as rapidly as poly(dA-dT) under comparable conditions. In contrast, the left-handed Z structure, formed by poly(dG-dC) in 3.0 M NaCl, is completely resistant to cleavage even though the same copolymer in the B structure at 15 mM NaCl is readily degraded. Poly(dA-dT) is rendered acid soluble at both salt concentrations at similar rates. The basis for the secondary structure specificity of the DNA cleavage reaction most likely resides in the requisite formation of a productive complex between (OP)2Cu+ and DNA during the course of this reaction. Previous studies have suggested that strand scission is due to oxidative destruction of the deoxyribose by hydroxyl radicals produced by the oxidation of DNA-bound Cu+ by H2O2. Apparently, the Z and A structures are unable to form a stable noncovalent complex with the same optimal geometry for cleavage as the B structure and are less susceptible to degradation. This artificial DNase activity may provide an approach to assess the formation of non-B-DNA structures in solution.