Atomic Resolution Structures of Dna and Dna Modified By Carcinogens

Abstract

We have developed new search techniques to deal with the multiple minimum problem in the computation of energy-minimized structures of DNA and DNA modified by carcinogens. These techniques have yielded atomic resolution views that agree with experimental results, and have permitted prediction of novel structures where data are lacking. In one strategy, wide searches of con formation space are employed in combination with sub unit buildup methods. The second strategy narrows the conformation space search to domains actually occupied by the molecule by means of measured distances that are employed as constraints in first-stage minimizations, but are finally released to yield unconstrained structures that are within bounds of the data. Such experimental structures are then also useful as starting forms for en ergy minimizations of chemically related substances for which no data are available. Structures for unmodified B and Z DNA and for DNA modified by benzo(a)pyrene diol-epoxides, which agree with experimental data, as well as structures of DNA modified by carcinogenic aro matic amines, for which detailed data are not available, have been computed by these methods.