THERMODYNAMICS OF DNA CONFORMATION &INTERACTIONS

A quantitative description of the energetics of nucleic acid
structure, conformations and interactions is prerequisite for a
detailed understanding of the biological function of DNA and RNA.
In this proposal, I plan to carry out systematic measurements of
the changes in volume accompanying fundamental physical processes
in nucleic acids, including base pairing, ion and ligand binding,
and 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. The role of hydration in these processes is assumed
to be important, but no such systematic values have been reported.
Effects of mismatches, nicks, as well as conformational
variations, including bends, hairpin loops, bulges and branches
will be included. Parameters will be determined from complete
thermodynamic profiles measured on sets of oligonucleotides of
appropriate sequence and structure, using a combination of
densimetric, calorimetric and spectroscopic techniques.
Comparisons of the centered values between deoxy and ribo oligomers
of similar sequence will be used to try to understand the
differences in thermodynamics of DNA and RNA. Combined densimetry,
calorimetry and spectroscopy will also be used to define the
thermodynamics of netropsin, distamycin A and actinomycin D binding
to oligonucleotides containing single binding sites. A high
sensitivity magnetic suspension densimeter will be constructed
following the design of Kupke, and used to make these measurements.