This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. RNA is an important and biological relevant molecule, which is involved in a number of critical cellular and regulatory functions. We are interested in studying the folding pathway and structural intermediate(s) of a group IIC intron from O. iheyensis ?a ~400 nt RNA. At the moment little is known about the specific features of this RNA molecule, and the structural characteristics that help it to traverse its folding landscape and correctly attain its functional native state. By observing the compaction that results from global structural transitions (Rg and Dmax) that accompany changes in the concentrations of biologically relevant and important mono- and divalent ions, and osmolytes we hope to better understand the architecture of this RNA. Moreover, SAXS data can be readily combined with information from biochemical experiments to yield nucleotide specific information on the sites of metal binding and localization within the RNA, which will illuminate what local structural transitions occur concurrently with global transformations.
The specific aims of this research is to establish a better understanding of the general processes of folding and RNA architecture as they relate to basic structural features of RNA. I have a background in utilizing NMR spectroscopy and residual dipolar coupling experiments to study the structure and dynamics of RNA junctions and motifs. I have attended a couple of short SAXS courses in the last year (2-day course by NSLS at BNL, and an 8-day course by EMBL-Hamburg at DESY), and I am currently working on new methods to study the structure and dynamics from analyses of RNA molecules through SAXS measurements and various biochemical footprinting data.
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