NMR ANALYSIS OF RNA STRUCTURE AND DYNAMICS

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The conformational and dynamical properties of RNA oligomers will be examined. Specifically, the sequences that will be studied in detail are: (1) three double helix forming oligomers, one for which the cognate DNA sequence has already been studied, one that may exhibit varying structure with temperature and a similar control sequence that should not vary, and (ii) variants of the binding site for the coat protein of R17 viral RNA that display differential affinities for the coat protein. The protein is involved in the translational repression of the R17-encoded replicase gene. These sequences will be used as models for fully base-paired RNA and hairpin/bulge loops that are common elements of folded RNA structures that occur in nature. unusual structural features will be related as fully as possible to their role in biological function. The principle tool is nuclear magnetic resonance and the project seeks to develop and refine applications of proton-proton nuclear. Overhauser enhancements and carbon-13 spectra. The former will be solution, and the latter will yield information on the internal dynamics of RNA. It is important to focus on RNA structures which are critical biomolecules in the expression of information coded in DNA. Over the years this project has helped create breakthrough in the synthesis of RNA oligomers and methods for assigning and evaluating their complex nmr spectra. This work as well as progress in other labs now make it feasible to determine three- dimensional structures in this difficult system. This project will contribute substantially to the exciting progress being made in the generation of detailed models of biomolecules from solution nmr data. It will also help develop and apply new methods where they can made a difference in the understanding of the control of genetic expression.