title: A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling.
abstract: In RNA site-directed spin labeling (SDSL) studies, structural and dynamic information at the individual RNA nucleotide level is derived from the observed electron paramagnetic resonance spectrum of a covalently attached nitroxide. A systematic approach for RNA SDSL is to establish a library that categorizes observed spectral lineshapes based on known RNA structures, thus enabling lineshape-based structure identification at any RNA site. To establish the first RNA SDSL library, selective secondary structure elements have been systematically engineered into a model RNA. Nitroxide lineshapes reporting features specific to each element were obtained utilizing a new avidin-tethering scheme for suppressing spectral effects due to uniform RNA tumbling. The data demonstrated two key features required for a SDSL library with a predicting power: (i) spectral divergence--distinctive lineshape for different elements; and (ii) spectral convergence--similar lineshape for the same element in different contexts. This sets the foundation for further RNA SDSL library development.
authors.affiliation: Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA. pzq@usc.edu
authors.forename: Peter Z
authors.initials: PZ
authors.lastname: Qin
authors.forename: Jennifer
authors.initials: J
authors.lastname: Iseri
authors.forename: Arisa
authors.initials: A
authors.lastname: Oki
mesh_terms: D001360:Avidin / Q000737:chemistry; D020029:Base Pairing; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D009589:Nitrogen Oxides / Q000737:chemistry; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013113:Spin Labels
chemical_list: D009589:Nitrogen Oxides; D013113:Spin Labels; D001360:Avidin; D012313:RNA; C039900:nitroxyl