Research

People

Publications

Protocols

SELECTED PUBLICATIONS

Reviews

• Woodson, S. A.  (2000) Recent insights on RNA folding mechanisms from catalytic RNA. Cell Mol. Life Sci. 57, 796-808.
• Thirumalai, D., Lee, N., Woodson, S. A. and Klimov, D. K.  (2001) Early events in RNA folding.  Annu. Rev. Phys. Chem. 52, 751-762.
• Woodson, S. A.  (2005) Metal ions and RNA folding:  a highly charged topic with a dynamic future.  Curr. Opin. Chem. Biol. 9, 104-109.
• Woodson, S. A. (2005) Structure and assembly of group I introns.  Curr. Opin. Struct. Biol. 15, 324-330.

Methods

• Ralston, C. Y., Sclavi, B., Sullivan, M., Deras, M. L., Woodson, S. A., Chance, M. R., and Brenowitz, M.  (2000) Time-resolved synchrotron X-ray footprinting and its application to RNA folding. Methods Enzymol. 317, 353-368.
• Deras, M. L., Woodson, S. A. , Brenowitz, M. (2001) Time-resolved hydroxyl radical footprinting of RNA with X-rays.  In Current Protocols in Nucleic Acid Chemistry (G. Glick, ed), Wiley Interscience, New York, pp. 11.6.1-11.6.24.
• Adilakshmi T., Lease, R. A. and Woodson, S. A. (2006) Hydroxyl radical footprinting in viv mapping macromolecular structures with synchrotron radiation.  Nucl. Acids Res. 34, e64.

Recent papers

• Rangan, P., Masquida, B., Westhof, E. and Woodson, S. A. (2003) Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme.  Proc. Natl. Acad. Sci. U.S.A. 100, 1574-1579.
• Rangan, P. and Woodson, S. A. (2003) Structural requirement for Mg2+ binding in the group I intron core.  J. Mol. Biol. 329, 229-238.
• Perez-Salas, U. A., Rangan, P., Krueger, S., Briber, R. M., Thirumalai, D. and Woodson, S. A. (2004) Compaction of a bacterial group I ribozyme coincides with the assembly of core helices.  Biochemistry 43, 1746-1753. 
• Koculi, E., Lee, N.-K., Thirumalai, D. and Woodson, S. A. (2004) Folding of the Tetrahymena ribozyme by polyamines:  importance of counterion valence and size.  J. Mol. Biol. 341, 27-36.
• Koduvayur, S. and Woodson, S. A. (2004) Intracellular folding of the Tetrahymena group I intron depends on exon sequence and promoter choice.  RNA 10, 1526-1532.
• Lease, R. A. and Woodson, S. A. (2004) Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA.  J. Mol. Biol. 344, 1211-1123.
• Adilakshmi T., Ramaswamy, P. and Woodson, S. A. (2005) Protein-independent folding pathway of the 16 S rRNA 5’ domain.  J. Mol. Biol. 351, 508-519.
• Chauhan, S., Caliskan, G. Briber, R. M., Perez-Salas, P., Rangan, P., Thirumalai, D. and Woodson, S. A. (2005) RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme.  J. Mol. Biol. 353, 1199-1209.
• Hopkins, J. F. and Woodson, S. A. (2005) Molecular beacons as probes of RNA unfolding under native conditions.  Nucl. Acids. Res. 33, 5763-5770.
• Caliskan, G., Hyeon, C., Perez-Salas, U., Briber, R. M., Woodson, S. A. and Thirumalai, D. (2005) Persistence length changes dramatically as RNA folds. Phys. Rev. Lett. 95, 268303.
• Caliskan, G., Briber, R. M., Thirumalai, D., Garcia-Sakai, V., Woodson, S. A. and Sokolov, A. P.  (2006) Dynamic transition in tRNA is solvent induced.  J. Amer. Chem. Soc. 128, 32-33.
• Koculi, E., Thirumalai, D. and Woodson, S. A. (2006) Counterion charge density determines the position and plasticity of RNA folding transition states.  J. Mol. Biol. 359, 446-454.