CAREER: NMR Methods for the Study of Functional Dynamics in Large RNAs

Regents Of The University Of Michigan - Ann Arbor, Ann Arbor MI

Investigators

Abstract

The function of virtually every regulatory RNA relies on molecular flexibility that allows it to fold into different conformations required during the course of assembly, catalysis, and regulation. Though NMR spectroscopy has proven to be one of the most powerful techniques for probing internal dynamics in proteins uniquely providing site-specific information, existing paradigms break down when applied to nucleic acids due to their unique spin physics and motional properties. The objective of this CAREER project is to develop and apply novel NMR methods for characterizing RNA dynamics from picosecond-to-millisecond timescales. At the heart of these methods is a domain elongation strategy that provides a means for interpreting spin relaxation data and residual dipolar couplings in terms of site-specific dynamical parameters. These methods will be generalized to allow studies of larger RNAs and used to investigate the network of internal motional modes that drives conformational adaptation in the transactivation response element (TAR) RNA upon recognition of cognate targets. This will then be followed by dynamic studies of a larger (80 nt), more complex thiamine pyrophosphate (TPP) riboswitch RNA domain from E. coli mRNA which represents a new class of regulatory RNAs that regulate gene expression by switching conformation upon target recognition. These investigations will yield the first site-specific characterization of internal motions in RNA providing fundamental new insight into how structure and dynamics come together to create function. By deepening our understanding of the physical principles governing RNA functional dynamics, this research will also benefit applications seeking to rationally control RNA activity, including the design of RNA sensors. The methodology can easily be adapted to study dynamics in DNA molecules. The main objective of the educational component is to foster greater awareness within the community about the excitement that surrounds scientific research and discovery. To this end, a one-day forum will be organized once a year at the University of Michigan that is open to the community and free of charge that presents and celebrates several major discoveries specifically as they pertain to the PI's research field of structural biology. From Linus Pauling's characterization of the chemical bond to the story surrounding the discovery of the DNA double helix, the forum will strive to explain in laymen's terms the intellectual strides that led to the discovery, and explore the human, historical, and cultural stories behind these achievements. The forum will include lectures followed by tours of state-of-the-art facilities used in biophysics research. The forum will be summarized in a pedagogical handbook which will be made available to the public via the internet. The forum is expected to enhance existing interactions between the Department of Chemistry and Biophysics Research Division at the University of Michigan and middle and high school students and teachers in the Ann Arbor and surrounding areas. In addition to one graduate student, this research project will be carried out by two undergraduate students currently in the PI's laboratory. This will help sustain a strong tradition of training undergraduate students in the PI's laboratory. This project is jointly supported by Molecular Biophysics in the Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences and the Experimental Physical Chemistry Program in the Division of Chemistry in the Mathematical and Physical Sciences Directorate.