Architecture of the Satellite Tobacco Mosaic Virus RNA Genome (2012)

Undergraduates: Eva Archer, Nicholas Watts, Rory O'Kane, Bangchen Wang

Faculty Advisor: Kevin Weeks
Department: Chemistry

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The genetic information necessary for replication of many viruses is encoded in single-stranded genomic RNA molecules. The RNA strand forms complex structures made up of helices, knots, and unpaired regions that contain additional information beyond the basic genetic code. Determining the forms of these structures can provide insight in how viruses reproduce, assemble, and interact with host organisms. The Satellite Tobacco Mosaic Virus (STMV) is an ideal model for understanding more complex and architecturally related viruses like polio and Dengue because of its small size and relatively simple genome. In this project, SHAPE chemistry and atomic force microscopy are used to probe the structure of the STMV genome and to understand how the RNA folds. A secondary structure with extensive long-range base pairing is proposed based on evidence from SHAPE data and atomic force microscopy imaging.