Nuclear magnetic resonance studies of the HIV-1 trans-activation response RNA element

[摘要] 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.

[发布机构] Rice University

[效力级别] Microbiology