We propose to systemically examine the thermodynamics and kinetics of the interaction of a series of positively charged oligopeptides with single-stranded (ss) homopolynucleotides and duplex DNA. These studies will involve the oligopeptides, (lys)n- 2-X-lys, (arg)n-2-X-arg (X=tyr or trp), (lys)n, and (arg)n of length n=3-10. Quantitative measurements of equilibrium binding constants will be made using changes in the fluorescence of the aromatic oligopeptides and changes in the circular dichroism spectra of the nucleic acids to monitor binding. Fluorescence stopped-flow techniques will be used to measure dissociation rate constants as a function of solution variables. Competition experiments will be used to study binding of the non-aromatic oligopeptides. Systematic studies of the equilibria of well defined, charged oligopeptide-ss nucleic acid interactions are severely needed to provide models for the electrostatic component of protein-ss nucleic acid interactions. Quantitative measurements of equilibrium binding constants as a function of solution variables, especially salt concentration, provide a necessary """"""""calibration"""""""" for the interpretation of similar studies of protein-nucleic acid interactions. In the absence of these model studies, one can not decompose the binding free energy into electrostatic vs. non-electrostatic contributions. A detailed, knowledge of the general effects of salt on the kinetics of model charged ligand-nucleic acid interactions are important for the interpretation of similar studies of the kinetics and mechanism of protein-nucleic acid interactions. These experimental studies will also be used to test the predictions of current theories, dealing with the interpretation of the salt dependence of equilibrium constants of charged ligand-nucleic acid interactions. A detailed thermodynamicanalysis of protein-nucleic acid interactions is dependent upon the availability of studies of model, charged ligands.
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