Professor
Thomas C. Jenkins Department of Biophysics
Krieger School of Arts & Sciences

swoodson@jhu.edu

402 Jenkins Hall
3400 N. Charles Street
Baltimore, MD 21218

Office: 410-516-2015
Lab: 410-516-7348

RNA molecules play a role in nearly every aspect of gene expression, including transcription, splicing, protein synthesis, and translational control. In order to perform these diverse functions, RNAs must fold into specific three-dimensional structures. RNA structures are dynamic and plastic, which allows them to form switches and regulators.

We are using physical and biochemical methods to understand how RNAs fold.  The three main projects in the lab are cooperative folding in group I ribozymes, assembly of the 30S ribosome, and interactions between small anti-sense regulatory RNAs and their mRNA targets. In living cells, RNAs fold as soon as they are transcribed. Important questions that remain to be addressed are how intracellular conditions influence the folding pattern of new transcripts, how proteins make the self-assembly of very large RNAs such as the ribosome more accurate, and how incorrectly folded or misassembled RNAs are recognized in the cell and targeted for degradation.

Rapid hydroxyl radical footprinting can probe individual tertiary contacts in RNA in milliseconds, yielding “snapshots” of the RNA structure as it forms. This method can also be used to probe the structures of RNPs inside the cell.  Stopped-flow fluorescence spectroscopy, small angle X-ray scattering, and neutron diffraction provide a global picture of RNA dynamics and stability. Native polyacrylamide gel electrophoresis is a simple and direct way of separating long-lived intermediates, and can be coupled to a wide range of biochemical methods.

Selected Publications
Ramaswamy, P., and S.A. Woodson.  (2009) S16 throws a conformational switch during assembly of 30S 5' domain. Nat. Struct. Mol. Biol. 16:438-445.

Roh, J.-H., R.M. Briber, A. Damjanovic, D. Thirumalai, S.A. Woodson, and A.P. Sokolov.  (2009) Dynamics of tRNA at different levels of hydration. Biophys. J. 96:2755-2762.

Adilakshmi, T., D. Bellur, and S.A. Woodson. (2008) Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly. Nature 455:1268-1272.

Chauhan, S., and S.A. Woodson. (2008) Tertiary interactions determine the accuracy of RNA folding. J. Amer. Chem. Soc. 130:1296-1303.

Soper, T. J., and S.A. Woodson. (2008) The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA. RNA 14:1907-1917.

Koculi, E., C. Hyeon, D. Thirumalai, and S.A. Woodson. (2007) Charge density of divalent metal ions determines RNA stability. J. Amer. Chem. Soc. 129:2676-2682.