Understanding the principles of DNA recognition by proteins and ligands is of central importance in biology and is directly relevant to a large body of problems associated with human disease. Similarly, RNA folding has become a problem of widespread interest, due to its relationship to fundamental biological processes and to new therapeutic approaches. The long range goal of the research described in the proposal is a detailed understanding of the relationships between structure and free energy that govern the structure and function of nucleic acids and their binding to various ligands and proteins. The specific goals of the proposed research are to study the large body of relevant structural and thermodynamic data that has accumulated in the past few years, and to use theoretical and computational methods to relate both types of measurements. For the DNA binding problem, a database of ligand and protein/DNA interfaces will be created. The GRASP program will be used to characterize the physical properties of the interfaces between ligand or proteins and DNA in complexes whose structures have been determined. Continuum methods will be used to calculate the binding free energies of the various complexes. In each case, the free energy will be partitioned into components with the goal of determining the major thermodynamic driving forces for the association of DNA with various ligands and proteins. Based on the accumulated data on structural parameters, calculated free energies and thermodynamic measurements, an attempt will be made to arrive at empirical rules that relate structure to free energy in DNA association reactions. For the RNA folding problem, Poisson-Boltzmann calculations will be used to describe the ion atmosphere and electrostatic potentials around all RNA molecules whose structures are known. These will then be related to measurements of the salt dependence of RNA conformational change. The electrostatic potentials will also be used as basis for understanding the large pKa shifts for some bases that have been observed in ribozymes. Continuum methods will be used to calculate and partition conformational free energies associated with the formation of RNA tertiary structure.
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