of the energetics of nucleic acid structure, conformational changes and interactions is one prerequisite for a detailed understanding of the biological function of nucleic acids. The role of hydration in determining the physical properties of nucleic acids is widely assumed to be important, but quantitative data are lacking. In this proposal, I plan to continue to carry out a series of systematic measurements of the changes in volume accompanying fundamental physical processes in nucleic acids, including base pairing, ion and ligand binding. I will correlate these values with heats and entropies determined on the same samples to provide a complete set of thermodynamic parameters for base-pairing of chains containing any sequence of complementary bases, and for sequence specific drug binding interactions. Effects of nearest-neighbor sequence, bulges, mismatches, as well as conformational variations, including bends, hairpin loops, and branches will be included in this description. complete thermodynamic profiles will be measured on sets of oligonucleotides of appropriate sequence and structure, using a combination of densimetric, calorimetric, spectroscopic and ultrasound velocity measurements. Using a similar thermodynamic approach, we will use the interaction of netropsin, distamycin A and bis-netropsin with short duplexes containing single and multiple binding sites to probe the hydration of the minor groove of B DNA, triplexes and the grooves of parallel DNA. The hydration of the major groove of B-DNA will be monitored using the complementary interaction of DNA oligomer chains with the major groove of homopurine/homopyrimidine polymer duplexes to form triplexes. Alternatively, the hydration of the immediate environment of the major groove can be followed with extrahelical bulges. The relative hydration of triplexes will be determined from complementary adiabatic compressibility measurements on these complexes as a function of temperature and sequence. Comparisons of the volume change between small sets of deoxy and ribo oligomers of similar sequence will be used to try to understand the differences in the thermodynamics of DNA and RNA. A high sensitivity temperature scanning velocimeter will be constructed for the measurement of ultrasound velocity as a function of temperature, which nicely complement the deltaV measurements.
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