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Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double‐helix

As a first step toward developing simulation models for studying the indirect mechanism of radiation damage to DNAs, we have carried out Brownian dynamics simulations to study the reactions of hydrated electrons with a 12‐base‐pair B‐DNA, (dA)12(dT)12, and with bases, monodeoxynucleotides, and polydeoxynucleotides. We first studied in detail the sensitivity of diffusion reaction rate constants to different model and simulation parameters. Based on the sensitivity studies, a set of model and simulation parameters was obtained for the final production runs. The use of this set of parameters reduced the computational costs but delivered reasonably reliable results. The calculated reaction rate constants were in qualitative agreement with experiments. For the DNA double‐helix, (dA)12(dT)12, the simulations demonstrated that hydrated electrons preferred to attack the two ends of the double‐helix. Electrostatic interactions between the DNA and the hydrated electrons make the T strand more susceptible to attack than the A strand. The increased reactivity of the T strand due to electrostatic interactions results from the increased reactivity of the C6 sites of the thymine bases, at the expense of the reactivity of the C8 sites of the adenine bases. The reactivity of the relatively buried reactive sites of the adenine and thymine bases are less affected by electrostatic interactions. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 888–901, 1997