Described are studies involving a new class of nucleoside analogs we have developed to test the importance of specific biomolecular interactions. Our nonpolar nucleoside isosteres are designed to closely mimic the shape of natural nucleosides, but to lack their ability to form polar hydrogen bonded or other electrostatic interactions. This work has led to valuable new insights into the roles of polar and steric interactions in DNA-DNA and protein-DNA binding, and in DNA replication. The long-term goals of this work are to utilize nonpolar nucleoside analogs to gain fundamental understanding of the importance of polar and steric effects in protein-DNA (RNA) binding and in DNA/RNA secondary structure. Over the shorter term covered by this proposal, the specific aims are (1) analysis of protein-DNA interactions for two transcription factors, and the study of DNA bending in the absence of protein; (2) examination of polar and steric effects in DNA replication and editing; and (3) study of the roles of polar and geometric effects in DNA mismatch repair. This work is important to biomedical research in two main ways. First, DNA-DNA and protein-DNA interactions are a fundamental part of most disease states, and so this work will help advance the basic understanding of the molecular basis of diseases, and eventually, in development of molecular therapies for disease. Second, a number of insights gained here may be more directly applied to future medical diagnostics and therapeutics, by offering new ways to modulate protein-DNA interactions and stabilize nucleic acid secondary structure.
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