MECHANISM AND KINETICS OF RNA FOLDING 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. 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. Folding of RNA molecules is critical for the functioning of a range of processes in cells, including gene regulation, viral RNA replication, and the assembly of RNA-protein complexes. As part of these processes, RNA must fold into a specific native structure. The folding of RNA starts with the neutralization of negatively charged phosphate groups in RNA by cations. The charge-screened RNA then collapses into compact intermediate state and subsequently folds into unique native structure with tertiary interactions. Characterization of folding pathway is an active area of research in order to understand the microscopic mechanisms of RNA folding. Outstanding questions on the folding process include: (1) details of the kinetics of folding nucleation and collapse, (2) the role of cations and RNA sequence in determining the specificity of collapse, and (3) the detailed distribution of the structural ensemble. In our work, we employ, time-resolved and static small angle X-ray scattering (SAXS) at BioCAT to study kinetics and thermodynamics of structural changes of a group I ribozyme from the bacterium Azoarcus. The work includes both wild type and mutants and compares the findings to the more widely studied Tetrahymena intron. The project will provide insight into the nucleation of RNA tertiary structures and make a comparison with theoretical models of electrostatic interactions in unfolded and folded RNAs.