Electrostatic effects on the rates of DNA-catalyzed reactions

Abstract

Abstract Diol-epoxide metabolites of many genotoxic polycyclic aromatic hydrocarbons are hydrolyzed to tetraols in a detoxification reaction. The hydrolysis reaction has both spontaneous and acid-catalyzed components; moreover, the reaction rate increases in the presence of DNA. The best studied of these diol epoxide metabolites are the trans 7,8 diol-9,10 epoxides of benzo[a]pyrene: anti -BPDE, the proximate carcinogen, in which the oxirane ring is anti with respect to the 7-hydroxyl group, and its syn diastereomer, syn -BPDE. Jerina and coworkers have studied the kinetics of the hydrolysis of syn - and anti -BPDE as a function of pH and DNA concentration and have measured the equilibrium constant for the formation of a noncovalent complex with DNA. They constructed a two-state model in which the diol epoxide is either free or statically bound: the free fraction is hydrolyzed with the same kinetics as it exhibits in solution without DNA; the bound diol epoxide reacts at faster rates. In this model, the dependence of the observed hydrolysis rates on both DNA concentration and pH is explained by using the rate constants, k 0 and k H , for reactions of the free diol epoxide, the rate constants, k cat 0 and k cat H , for the bound molecule, and the binding constant, K eq . The present work uses an acidic-domain interpretation of the two-state model to explain the catalytic effect of DNA on the acid-catalyzed hydrolysis of syn - and anti -BPDE. Postulating that the rate enhancement is a result of acidic domains at the DNA surface, we assumed the relationship k cat H = k H [H + ] b , where [H + ] b is the hydrogen ion concentration near the bound molecule. Using numerical solutions to the Poisson-Boltzmann equation, the pH dependence of acidic domains at the surface of the polyelectrolyte, DNA, was calculated. Energy-minimization calculations were used to estimate the conformations of diol epoxide-DNA intercalation complexes. Poisson-Boltzmann (PB) calculations on these structures yielded hydrogen-ion concentrations near the epoxide group consistent with the k cat H /k H ratio over a range of added-salt concentrations. The results strongly suggest that DNA catalysis of diol-epoxide hydrolysis is a polyelectrolyte effect. The mechanisms and rate constants observed for the acid-catalyzed hydrolysis in the absence of DNA are consistent with the increase in the rate constant induced by DNA. It may be concluded that the catalysis is primarily an effect of the acidic domains in the surface grooves of the nucleic acid.