Rates of Spontaneous Disintegration of DNA and the Rate Enhancements Produced by DNA Glycosylases and Deaminases

Abstract

To estimate the relative importance of alternate routes of spontaneous degradation of DNA and the rate enhancements produced by enzymes catalyzing these reactions, rate constants and thermodynamic activation parameters for the degradation of 2‘-deoxynucleosides at 25 °C were determined by extrapolation of rates observed in the temperature range between 90 and 200 °C in neutral phosphate buffer. Rates of deamination of 2‘-deoxycytidine, 1-methylcytosine, and cytidine were found to be identical within experimental error (t_1/2 ≈ 20 years, 37 °C). Rate constants for deamination of 2‘-deoxyadenosine and 2‘-deoxyguanosine, which could not be determined directly because of rapid glycoside cleavage, were estimated by assuming that methyl replacement should generate reasonable model substrates. The rates of deamination of 9-methyladenine and 9-methylguanine were found to be similar to each other (t_1/2 ≈ 6000 years, 37 °C) and ∼10²-fold slower than the rates of glycoside cleavage in 2‘-deoxyadenosine and 2‘-deoxyguanosine. The deamination of 2‘-deoxyadenosine, 2‘-deoxyguanosine, and 2‘-deoxycytidine led to accelerated rates of glycoside cleavage. In the exceptional case of 2‘-deoxycytidine, deamination and glycoside hydrolysis proceed at very similar rates at all temperatures. Glycoside cleavage proceeds with half-times ranging from 4 years for 2‘-deoxyinosine to 40 years for 2‘-deoxycytidine (37 °C). The rate enhancements produced by DNA glycosylases, estimated by comparison with the rates of these uncatalyzed reactions, are found to be substantially smaller than those produced by deaminases and staphylococcal nuclease.