The immediate objective of this research is to obtain the best procedures for stimulating the ion and solvent environment of crystalline DNA, initially and particularly z-DNA. This is a particular problem due to the high charge density and large surface area of nucleic acids. The longer range objective is to develop a protocol which will be applicable for stimulating the ion and solvent environment of nucleic acids in general in both crystalline and non-crystalline environments. The energies of the non-bonding interaction with the ion and solvent environment are typically greater than the internal non-bonding energies for nucleic acids. Accordingly, a reliable remodeling of the nucleic acid requires an accurate modeling of the solvent. The ability to understand and model the structure of the interactions of nucleic acids will lead to more reliable drug design, a better understanding of the modes of interactions of the numerous proteins that interact with nucleic acids and of the folding and compaction of nucleic acids. Crystalline Z-DNA has been selected for these initial studies since we have extensive, very high resolution x-ray diffraction data on the crystals data on the crystals which has provided us with a much more detailed view of the ion and solvent environment than is available for other structures. This in turn will provide a reliable basis for assessing the quality of our simulations.
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