DETERMINING THE FOLDED AND UNFOLDED STRUCTURE OF THE HIV-1 TAR RNA USING SAXS

Stanford University, Stanford CA

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. TAR RNA from HIV-1 takes the form of a common structural motif in RNA folding, its conformational properties are relevant to the understanding of most structured RNAs. Moreover, the TAR RNA plays a crucial role in the lifecycle of HIV;knowledge about its structure will inform studies of its function, and contribute to the search for an HIV drug. The goal of this project is to measure the counterion-induced folding of the transactivation response element (TAR) from human immunodeficiency virus (HIV) using small-angle x-ray scattering (SAXS). The structure of HIV TAR will be probed in its unfolded state, as well as in various ligand and counterion-induced folded conformations. The structures obtained will be used to better understand the folding landscape of HIV TAR and to provide experimental limits for existing models.