The primary goal of the proposed research is a detailed understanding of the relationships between structure and free energy that govern conformational changes and binding reactions of nucleic acids. The research involves the continued development of theoretical approaches and their application to problems of biological interest. The basic approach is to describe solute molecules in atomic detail while employing a macroscopic description of the solvent. Electrostatic potentials are obtained from finite difference solutions to the Poisson-Boltzmann equation (the FDPB method). The potentials are then used to calculate electrostatic free energies, using an expression derived in the previous funding period. Non-polar contributions are calculated from free energy/surface area relationships. The applications will focus on three classes of problems. 1) Salt effects on the binding of ligands to DNA. Electrostatic potentials around different forms of DNA and RNA will be calculated and compared to results obtained from spin label experiments. The salt dependence of the association constant of drugs that bind in the minor groove, as well as of a number of proteins, will be calculated and compared to experiment. The pH dependence of protein-DNA recognition will also be considered. Model calculations will be used to define possible mechanisms of sequence- specific recognition. The relationship of the total free energy obtained from the PB equation to the predictions of the widely used counterion condensation theory will be explored. 2) Salt independent contributions to binding will be calculated. Experimental comparisons will be made to the measured relative binding free energies of different drugs, and to the results of mutation experiments which modify the binding of different proteins to DNA. In this context an attempt will be made to understand free energy changes associated with hydrophobic and hydrogen bonding mutations. 3) General methods to include solvent and salt effects in the conformational analysis of nucleic acids will be developed. Solvation free energies will be added to the gas phase energies obtained from standard force fields. The effects of solvent and base sequence on the relative free energies of A, B and Z DNA will be calculated. The effects of base sequence on the stability of DNA and RNA loops will also be considered. The health relatedness of these problems results primarily from the fundamental biological importance of understanding nucleic acid structure and function. In addition, drugs that bind to DNA have many therapeutic applications.
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