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. Understanding the folding mechanism of RNA is crucial for understanding biological processes such as gene regulation, viral RNA replication, and the assembly of RNA-protein complexes. Folding of RNAs is driven by neutralization of phosphate charge by cations. In the presence of the cations, RNAs fold into native tertiary structure following an initial collapse into compact intermediates. It is believed that different folding pathways partition the RNA population, some of which is kinetically trapped in misfolded intermediates. However, the details of the RNA folding mechanisms remain unclear, including the following important questions: (1) the kinetic mechanism of folding nucleation and collapse, (2) the role of cations and RNA sequence in determining specificity of collapse, and (3) the breadth of the structural ensemble. In order to address these questions, we are using time-resolved and static small angle X-ray scattering (SAXS) at BioCAT on a group I ribozyme from the bacterium Azoarcus. The results will give insight into the early stages of RNA folding and provide experimental tests of theoretical models of electrostatic interactions in unfolded and folded RNAs.