A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling |
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Authors: | Qin Peter Z Iseri Jennifer Oki Arisa |
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Institution: | Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA. pzq@usc.edu |
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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. |
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Keywords: | RNA Site-directed spin labeling Secondary structure Lineshape Library |
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