dc.contributor.advisor Olson, John S. Xi, Zhijian (David) 2009-06-03T23:56:21Z 2009-06-03T23:56:21Z 1995 https://hdl.handle.net/1911/16901 Multidimensional NMR techniques and $\sp{13}$C/$\sp{15}$N isotope labelling have been used to study the structural and dynamic properties of the trans-activation response (TAR) RNA element from HIV-1. Theoretical analysis of the anticodon loop region of yeast tRNA was first performed. High resolution structures were obtainable when coarse distance constraints and the CHARMm forcefield were employed. A medium resolution NMR structure of the active $\Delta$TAR 29mer RNA was also determined, revealing interesting conformations in the bulge and loop regions. The local atomic dynamics of $\Delta$TAR were examined with two-dimensional $\sp{13}$C-$\sp1$H NMR relaxation methods. Pulse sequences were developed to measure relaxation times in fully coupled RNA spin systems. Observed T$\sb1$, T$\sb2$ and NOE values were fit to various forms of the Lipari-Szabo motional model. The resulting order parameters and internal correlation times correlate strongly with local structural features of $\Delta$TAR. Studies on the solution structure of one natural occurring mutant of TAR, the HIVRF loop sequence, indicate that the TAR structure may adopt a more compact loop structure that cannot be fully determined with current NMR methods. 202 p. application/pdf eng Molecular biologyMicrobiologyBiophysicsBiology Nuclear magnetic resonance studies of the HIV-1 trans-activation response RNA element Thesis Text Biology Natural Sciences Rice University Doctoral Doctor of Philosophy Xi, Zhijian (David). "Nuclear magnetic resonance studies of the HIV-1 trans-activation response RNA element." (1995) Diss., Rice University. https://hdl.handle.net/1911/16901.
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