Reactions of divalent metal ions with the oxidant Ru(tpy)(bpy)O2+ (bpy = 2,2'-bipyridine; tpy = 2,2',2"-terpyridine) in the presence of DNA were studied by gel electrophoresis and optical absorption. The reaction of Mn2+ with Ru(tpy)(bpy)O2+ produced a transient intermediate with a new absorption at 531 nm and a second-order rats constant of 1300 +/- 200 M-1 s(-1). This rate constant is 100 times greater than that of the reaction with GMP (guanosine 5'-monophosphate), suggesting that Mn2+ is a kinetically competent inhibitor of DNA oxidation. A second-order rate constant of 1.1 +/- 0.2 M-1 s(-1) was measured for the reduction of Ru(tpy)(bpy)OH2+ by Mn2+; this relationship of rate constants for Ru(IV) and Ru(III) by the same substrate is typical for this oxidant. Plasmid gel electrophoresis demonstrated that Mn2+ was a competent inhibitor in the conversion of the supercoiled form of phi X174 plasmid DNA to the circular form. The Mg2+ and Ni2+ ions, which do not react with the oxidant but do compete for electrostatic binding to the biopolymer, did not inhibit plasmid cleavage. In high-resolution electrophoresis experiments, the extent of quenching of oxidation by Mn2+ in the sequences d[5'-TTCAACA G(16)TG(18)TTTG(22)AA] and r[5'GUUCUUG(7)CUUCAACG(16)UG(18)UUUG(22)AACG(26)G(27)AAC] was dependent on the oligomer structure, where cleavage of residues in the hairpin loop was inhibited most efficiently. In contrast, quenching by Mg2+, Ni2+, and Co2+ was much less efficient and occurred only in the double-stranded regions. The selectivity of inhibition by Mn2+ could be attributed to differential rates of deactivation of the bound Ru(tpy)(bpy)O2+ oxidant.