Prof. Peter Z. Qin, University of Southern California

Site-Directed Spin Labeling Studies of Nucleic Acids

In site-directed spin labeling (SDSL), a stable nitroxide radical is attached at a specific location within a macro-molecule, and structural and dynamic information at the labeling site is obtained via electron paramagnetic resonance (EPR) spectroscopy. I will present work on development and application of SDSL for mapping global structures of nucleic acids. These studies center on an R5 nitroxide probe that can be attached, in an efficient and cost-effective manner, at a specific nucleotide of any given RNA and DNA. State-of-art pulse EPR techniques have been used to successfully measure nanometer distances (20 - 50 Å) between a pair of R5's attached in DNA and RNA, and an efficient program, called NASNOX, has been established for correlating the inter-R5 distances to the parent nucleic acid structure. Together, the R5 probe, the pulse EPR method, and the NASNOX program constitute a tool-kit for un-restricted global structural mapping of nucleic acids and protein/nucleic acid complexes. This tool-kit is being utilized to map the global structure of the packaging RNA (pRNA) in the phi29 bacteriophage DNA packaging motor, which is the strongest known bio-molecular motor. The pRNA forms a ring-shaped complex that is indispensable in motor ATPase activity, yet structural information on pRNA is lacking. We are using the SDSL tool-kit to obtain pRNA inter-helical distances. These constraints are used to determine the spatial packing of the helices and define the global structure of functionally relevant pRNA complexes. This represents the first application of SDSL to study an RNA with unknown structure.

For more information contact Dr. Nick Hud (404-385-1162).