COMBINED SAXS & NMR TO STUDY THE STRUCTURE & DYNAMICS OF LARGE RNA MOLECULES

Illinois Institute Of Technology, Chicago IL

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. One of the greatest advances in frontier biology in the past decade is the discovery of a vast variety of roles non-coding RNA played in biological processes. However, our knowledge about the three-dimensional structures of RNA is limited for various reasons. RNAs are difficult to crystallize;RNAs with normal functional sizes are too large for structure determination using the current solution NMR methods. Recently, we have developed a novel method that uses NMR spectroscopy, synchrotron-based small angle X-ray scattering (SAXS) and a novel computational program to solve structures of large RNAs in solution. In general, a well-folded RNA structure is packed with a number of A-form duplexes. The global structure of RNAs can be determined if the relative orientation and position of those duplexes are known. We derive the relative orientation of duplexes using residual dipolar coupling-structure periodicity correlation and restrain the relative positions of duplexes using SAXS data. We have demonstrated this method using adenine-riboA switch RNA (71nt). A manuscript that describes the methodology is currently under review by Proceedings of the National Academy of Science. Furthermore, we have applied the method to solve the global structure of a 102-nt RNA fragment that plays a role as a translational enhancer in turnip crinkle virus (tcv) RNA and a manuscript for the latter is currently in preparation. Our research is funded by an NIH intramural research grant to YXW*. The access to the synchrotron beamline at APS has made this new methodology development possible.