The Effect of Water on Sequence Specific DNA Recognition

Furman University, Greenville SC

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Abstract

DESCRIPTION (provided by applicant): The interaction of a ligand with DNA is central to many biological processes, and these studies will focus on the role of water in the interaction of small molecule drugs with DNA. DNA sequence recognition by small molecules offers the potential to influence the regulatory control of genes and thus confer a therapeutic effect. While a number of factors contribute to sequence recognition, the role of water is the focus of these studies. Thermodynamic, structural, and kinetic studies will be used to evaluate hydration changes in these reactions. I. A rapid screening approach will be developed to assess the relationship between ligand binding, solvent exchange, and the DNA and ligand structure. The osmotic pressure exerted by neutral osmolytes will be used to perturb the water population in the vicinity of the DNA and, hence, will affect the stability of complexes that are sensitive to hydration. These studies will consider DNA sequence and structrure. II. On the basis of the rapid screening approach, association reactions that exhibit signficant water exchange will be studied more thoroughly. First, the stoichiometry of the water exchange will be measured via the affect of osmotic stress on the ligand - DNA equilibrium. Second, the contribution of water exchange to the enthalpy change will be measured using the difference in the hydrogen bond strength for D20 vs. H20. These two techiques will also be used to examine how the ligand stoichiometry (monomer vs dimer) influences the solvent reorganization. III. Using fluorescence correlation spectroscopy, the rate constants for ligand exchange between different DNA sequences will be measured. Using the variation of the rate constants with osmotic pressure, the number of waters exchanged in the transition state will be determined. These studies determine the involvement of water exchange in the mechanism, thus complementing the thermodynamic studies.