This is a renewal application for an existing grant. This proposal aims to measure complete thermodynamic profiles including hydration effects for a variety of DNA duplexes, some with modified phosphates, and for a number of DNA or DNA/RNA duplexes with intercalated or covalently bound ligands. Experimental methods include temperature and pressure dependent UV and CD spectroscopy, high sensitivity differential scanning calorimetry, and titration calorimetry. In particular, Dr. Marky proposes: 1) to characterize the role of counterions (Cs+ ,Na+ , K+ , Mg++) in the stability of telomeric and centromeric model sequences. 2) to determine the overall hydration of hairpins (stem-loop structures) containing bulges and mismatches and to characterize hydration effects from interactions with intercalating agents. Complete thermodynamics profiles (deltaG, deltaH, delta S and deltaV) will be obtained. 3) to determine differences in thermodynamic behavior, including hydration, of DNA, RNA and mixed duplexes. 4) to thermodynamically characterize, in terms of binding mode and conformation, the hydration effects from placing covalently bound hydrophobic moieties in oligomer duplexes. 5. to obtain complete thermodynamic profiles, including heat capacity effects, for side-by-side binding of cross-linked lexitropsins to the minor groove of DNA. 6. to determine the electrostatic and hydration contributions in the formation of DNA bent structures.
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