Structural Dynamics of Protein-RNA Complexes

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DESCRIPTION (provided by applicant): Group I introns are non-coding regions in RNA genes that are capable of excision through a self-splicing mechanism. The introns must fold to the correct native structure to catalyze the reaction despite thermodynamic and kinetic challenges. Two of the group I introns from the Neurospora crassa mitochondrial RNA are dependent on a protein cofactor, CYT-18, to fold to the correct structure for self-splicing. A second protein, CYT-19, accelerates the splicing rate for these protein-bound introns. To investigate the multiprotein-RNA interactions in Neuospora crassa, ribozymes derived from the introns will be examined using single molecule fluorescence. Through site-specific dye-labeling of the RNA, the structural dynamics of specific domains and single tertiary interactions for individual molecules will be monitored. Structural transitions associated with the catalytically active conformation will be followed for the protein-RNA complexes. The work will help to dissect the evolutionary role of proteins in compensating for deficiencies in RNA folding. The techniques developed in exploring the RNA-protein interactions in this model system may aid in providing the basis for future methodologies to probe more complicated health-related systems.