CAREER: Structure, Dynamics, and Function of the Packaging RNA Studied using Site-directed Spin Labeling

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Nucleic acids are essential in biological processes, and information on nucleic acids structure and conformational changes is critical in understanding their functions. This project will establish a new method for investigating nucleic acids conformations. The method is based on the site-directed spin labeling (SDSL) technique, where structural and dynamic information is derived from a stable nitroxide radical attached at a specific site of a macro-molecule. The research will explore a nitroxide probe that can be attached, in an efficient and cost-effective manner, to arbitrary nucleic acid sequences. Nanometer distances between a pair of such nitroxides will be measured, and the resulting data will be utilized to map the global structures of nucleic acids. To demonstrate the SDSL methods, global structures of nucleic acid molecules without prior known high-resolution structures will be studied. These include the packaging RNA that plays an essential role in the strongest bio-molecular motor known today : the phi29 DNA packaging motor. The studies will set a precedent for a wide range of SDSL studies on nucleic acids and nucleic acid/protein complexes without prior high-resolution structures. Broader Impacts: The PI will establish innovative, inter-disciplinary programs that integrate research and teaching at both the undergraduate and graduate level. A new general education course, called "Genes, Life, and Society", will be developed. The course will present the nature of genes with rigorous and precise molecular descriptions of nucleic acids structure and function, and will link the scientific concepts with contemporary societal issues such as evolution and diversity of our society. The course will utilize "BioSIGHT", a multi-media teaching platform being developed at an NSF-funded center at USC. The class will target a large population of science and non-science students, and will be used in outreach programs to high-school teachers through public lectures and web sites.