Determining the Folded and Unfolded Structure of the HIV TAR RNA Using Small-Angle X-ray Scattering

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Abstract/Contents

Abstract: In biological macromolecules, such as proteins or RNA, structure determines function. While most RNA primary sequences code for proteins, some RNA, called non-coding RNA, fold into a range of tertiary structures to regulate transcription of the coding RNA. These tertiary structures can be influenced by several environmental factors, including counterion concentrations and ligands that bind to specific sites on the RNA and induce folding. Thus knowledge of the dynamic range of an RNA molecule in solution is crucial to understanding its function in vivo. In this experiment, the structure and folding landscape of the transactivation response element (TAR) RNA from the human immunodeficiency virus (HIV) was probed using small-angle x-ray scattering (SAXS) techniques. TAR takes the form of a common structural motif in RNA folding, so 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 could contribute to the search for an HIV drug. In the first SAXS measurement of HIV TAR, we probed the structure of the TAR RNA in its unfolded state, as well as in several different ligand and counterion-induced folded conformations.

Type of resource	text
Date created	2011

Author	Tang, Maxine Chi-Leung
Department	Stanford University, Department of Physics
Primary advisor	Doniach, Sebastian
Advisor	Das, Rhiju

Subject	transactivation response element
Subject	TAR RNA
Subject	small-angle x-ray scattering
Subject	SAXS
Genre	Thesis

Location	https://purl.stanford.edu/qm274fz0921

Use and reproduction: User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
License: This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).

Preferred Citation: Tang, Maxine (2011). Determining the folded and unfolded structure of the HIV TAR RNA using small-angle x-ray scattering. Stanford Digital Repository. Available at http://purl.stanford.edu/qm274fz0921.

Undergraduate Theses, Department of Physics

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