Kinetics of metal-mediated one-electron oxidation of guanine in polymeric DNA and in oligonucleotides containing trinucleotide repeat sequences

The oxidation of guanines in DNA by Ru(III) is investigated by catalytic el ectrochemistry and stopped-flow spectrophotometry. The reactions of calf th ymus DNA (20% guanide) and herring testes DNA (25% guanine) with Ru(bpy)(3) (3+) (bpy = 2,2'-bipyridine) show biexponential decays in stopped-flow spec trophotometric experiments with the fast and slow components in 2:1 ratios and average rate constants in 880 mM NaCl of <k > = 18 700 M-1 s(-1) for ca lf thymus DNA and <k > = 24 600 M-1 s(-1) for herring testes DNA. The highe r rate constant for the more guanine-rich DNA is possibly due to a higher d ensity of electron-rich guanine multiplets. The observation of a biexponent ial decay is incorporated into digital simulations of the catalytic voltamm ograms observed for Ru(bpy)(3)(2+) in the presence of DNA. For both DNAs, t he rates observed by voltammetry are somewhat slower than those observed by stopped-flow spectrophotometry and the dependence of the rate constants on scan rate using the biexponential model is less pronounced than when only one decay is treated, supporting the notion that the scan rate dependence a rises from the multiphasic decay. At low salt concentrations, where binding of the metal complex to DNA increases the effective catalytic rate constan t, rates can be measured by stopped-flow spectrophotometry only with a less oxidizing complex, Fe(bpy)(3)(3+/2+), which yields trends in the rate cons tants similar to those observed for the case of Ru(bpy)33+/2+ at high ionic strength.. Oligonucleotides base; on the trinucleotide repeat sequences (A GT)(n) and (GAA)(n) produce significant catalytic currents, which are readi ly interpreted in terms of the guanine concentration and the secondary stru cture discerned from gel electrophoresis experiments. These experiments may provide a basis for sensing secondary structures and repeat numbers in bio logically relevant DNAs.