Our long-term goal is to develop an understanding of the molecular forces that dictate and control the affinity and specificity of drug binding to DNA. Such a molecular understanding of drug-DNA interactions is a prerequisite for the development of a rational basis for drug design. Our approach is to determine complete thermodynamic binding profiles for the complexation of several antitumor and antiviral drugs to various DNA host duplexes. Specifically, spectroscopy and batch calorimetry will be employed to characterize thermodynamically the binding event as a function of the structure of the drug and the sequence of both oligomeric and polymeric host DNA's. These thermodynamic binding profiles for each drug will allow us to: define the nature of the forces that drive complexation and predict the temperature-dependent stability of the complex; determine the thermodynamic origin of sequence binding preferences; define the thermodynamic basis for cooperative binding; evaluate the role of specific structural features of the drug by comparing the binding data on a series of drug analogues; correlate the thermodynamic data with the mode of binding and the molecular picture of the complex; resolve drug-induced conformational changes from local, specific drug-DNA interactions by comparing binding data on corresponding oligomeric and polymeric DNA hosts; evaluate the thermodynamic basis for drug synergism by comparing binding data for a drug in the presence and absence of other drugs. Differential scanning calorimetry will be used to detect, monitor, and thermodynamically characterize the influence of drug binding on the melting behavior of the host duplex. In particular, the size of the cooperative melting unit for each host duplex will be determined in the presence and absence of each drug. This parameter will provide a measure of the influence of drug binding and base sequence on the ability of a polymer chain to propagate molecular distortions -- a property which undoubtedly is of great importance in numerous biological processes. Calorimetry represents the only experimental method by which the relevant thermodynamic data can be obtained in a direct and model-independent manner. In conjunction with standard spectroscopic techniques, this proposal is designed to exploit the unique powers of batch and differential scanning calorimetry to obtain complete thermodynamic and extra-thermodynamic profiles of the solution properties of drug binding and the resultant drug-DNA complexes.
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