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

Abstract

The oxidation of guanines in DNA by Ru(III) is investigated by catalytic electrochemistry and stopped-flow spectrophotometry. The reactions of calf thymus DNA (20% guanine) and herring testes DNA (25% guanine) with Ru(bpy)3(3+) (bpy = 2,2'-bipyridine) show biexponential decays in stopped-flow spectrophotometric 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 calf thymus DNA and <k> = 24,600 M-1 s-1 for herring testes DNA. The higher rate constant for the more guanine-rich DNA is possibly due to a higher density of electron-rich guanine multiplets. The observation of a biexponential decay is incorporated into digital simulations of the catalytic voltammograms observed for Ru(bpy)3(2+) in the presence of DNA. For both DNAs, the 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 arises from the multiphasic decay. At low salt concentrations, where binding of the metal complex to DNA increases the effective catalytic rate constant, 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 constants similar to those observed for the case of Ru(bpy)3(3+/2+) at high ionic strength. Oligonucleotides based on the trinucleotide repeat sequences (AGT)n and (GAA)n produce significant catalytic currents, which are readily interpreted in terms of the guanine concentration and the secondary structure discerned from gel electrophoresis experiments. These experiments may provide a basis for sensing secondary structures and repeat numbers in biologically relevant DNAs.