Cleavage of DNA with methidiumpropyl-EDTA-iron(II): reaction conditions and product analyses

The synthesis of methidiumpropyl-EDTA (MPE) is described. The binding affinities of MPE, MPE•Ni(II), and MPE•Mg(II) to calf thymus DNA are 2.4 X 10^4 M^(-1), 1.5 X 10^5 M^(-1), and 1.2 X 10^5 M^-1), respectively, in 50 mM NaCl, pH 7.4. The binding site size is two base pairs. MPE•Mg(II) unwinds PM2 DNA 11 ± 3° per bound molecule. MPE•Fe(II) in the presence of O_2 efficiently cleaves DNA and with low sequence specificity. Reducing agents significantly enhance the efficiency of the cleavage reaction in the order sodium ascorbate > dithiothreitol > NADPH. At concentrations of 0.1-0.01 µM in MPE•Fe(II) and 10 µM in DNA base pairs, optimum ascorbate and dithiothreitol concentrations for DNA cleavage are 1-5 mM. Efficient cleavage of DNA (10 µM in base pairs) with MPE•Fe(II) (0.1-0.01 µM) occurs over a pH range of 7-10 with the optimum at 7.4 (Tris-HC1 buffer). The optimum cleavage time is 3.5 h (22 °C). DNA cleavage is efficient in a Na^+ ion concentration range of 5 mM to 1 M, with the optimum at 5 mM NaCl. The number of single-strand scissions on supercoiled DNA per MPE•Fe(II) under optimum conditions is 1.4. Metals such as Co(II), Mg(II), Ni(II), and Zn(II) inhibit strand scission by MPE. The released products from DNA cleavage by MPE•Fe(II) are the four nucleotide bases. The DNA termini at the cleavage site are 5'-phosphate and roughly equal proportions of 3'-phosphate and 3'-(phosphogiycolic acid). The products are consistent with the oxidative degradation of the deoxyribose ring of the DNA backbone, most likely by hydroxy radical