CONFORMATIONAL ANALYSIS OF RIBOSWITCH APTAMERS BY SAXS

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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. Current year GUP-21939: This GUP is a follow-up to GUP11627(2008) and GUP12457 (2009) in which we examined the proposed general features of riboswitch conformational change upon binding cognate small-molecules. Riboswitches are gene-regulatory mRNA domains that respond to the intracellular concentration of their cognate small molecules by modulating transcription or translation in bacteria and pre-mRNA splicing or polyadenylation in eukaryotes. For all riboswitch classes examined, phylogenetic sequence analyses delineate a segment of highly conserved sequence that is necessary and sufficient for specific in vitro binding to their cognate metabolites. These specific binding domains, or aptamers, have been the central focus of studies investigating riboswitch mechanism and function. Conformational changes are thought to be an integral part of riboswitch function. Small angle X-ray scattering is a technique to probe the global nature of such conformational changes. Recently, several labs have published papers utilizing this technique to understand the metabolite-induced structural response of several riboswitch RNA. The current proposal is related to GUP12457 and GUP11627, both entitled "Investigating the proposed 'switching' mechanism of various riboswitches". The previous GUPs, for which beamtime was allocated, focused on examining the proposed general features of riboswitch function. SAXS analyses revealed idiosyncratic responses of various riboswitches to their respective small-molecule effectors as described in our recent publications (Baird and Ferre-D'Amare, RNA, 2010; Kulshina et al, NSMB, 2009).