Structure and dynamics of DNA hairpins

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An integrated solid-state and solution NMR study of RNA and DNA will be conducted, focusing on the chemical shift as a primary spectroscopic observable. 15N and 13C shielding tensors will be experimentally determined for the major DNA and RNA species and conformations, and these will be supplemented and extended by quantum chemical calculations, to give a comprehensive picture of the relationship between chemical shift and conformation in nucleic acids: The extent to and accuracy with which conformation can be determined from chemical shift and shielding tensors data by the methods of discriminant analysis, and this statistical information will be incorporated as a weighting factor in refinement protocols for NMR structure determination. Chemical shift spectra will be collected for a small set of DNA hairpins and minihairpins in the solid, isotropic solution and oriented solution state, and the effect of dynamics and of difference between the crystalline and solution structure on the NMR spectrum quantified. The end result will it is hoped be (i) improved methods for determining DNA and RNA structure and dynamics and (ii) a full understanding of the structure and dynamics or DNA hairpins, which have been implicated in a number of normal and disease states.