Pan T. X. Li

• Single Molecule Manipulation and Detection
• Mechanical RNA Folding
• Protein-RNA Interaction

Our goal is to understand the fundamental principles that govern the folding of RNA and to apply such knowledge to engineer macromolecular assembly. Folding of an RNA molecule can be viewed as a biased diffusion over its folding energy landscape. Such energy landscape can be characterized by following molecular trajectories of individual molecules. Using optical tweezers technique, we stretch and relax single RNA molecules. This rubber-band-like experiment allows us to apply picoNewton (10 -7 gram) force to unfold the RNA structure and measure changes in the molecular extension with nanometer precision. Currently, we focus on three areas: (1) Force induced misfolding. By changing force in different ways, we can induce RNA molecules to fall into kinetic traps and then rescue them into the native structure. This method provides a unique way to survey the topography of the folding energy landscape. (2) RNA kissing complex, a tertiary structure formed between loops of two hairpins. By studying the formation and stability of such structures under mechanical tension, we measure the strength of tertiary interactions and the constraints of their formation. (3) Detecting ligand and protein binding to RNA structures by optical tweezers. We have developed a new method to pinpoint structural domains that bind to ligand or protein. Using this approach, we are developing new type of biosensors and drug screening strategy.

• Li, P.T.X. and Tinoco, I., Jr. (2009) Mechanical unfolding of two DIS RNA kissing complexes from HIV-1. J. Mol. Biol., 386, 1343-56.
• Li, P.T.X. and Tinoco, I., Jr. (2009) Thermodynamics and kinetics of RNA unfolding and refolding. In Walter, N, Woodson, SA and Batey, R., "Non-Protein Coding RNAs" Springer Series in Biophysics, vol. 13.
• Li, P.T.X., Vieregg, J. and Tinoco, I., Jr. (2008) How RNA unfolds and refolds. Annu. Rev. Biochem.77, 27.1-27.4
• Li, P.T.X., Bustamante, C., and Tinoco, I., Jr. (2007) Real-time control of the energy landscape by force directs the folding of RNA molecules. Proc. Natl. Acad. Sci. U.S.A. 104, 15847-15852
• Wen, J.-D., Manosas, M., Li, P.T.X., Smith, S.B., Bustamante, C., Ritort, F., and Tinoco, I., Jr. (2007)Force unfolding kinetics of RNA using laser tweezers. I. Effects of experimental variables on measured results. Biophys. J. 92, 2996-3009
• Manosas, M., Wen, J.-D., Li, P.T.X., Smith, S.B., Bustamante, C., Tinoco, I., Jr., and Ritort, F. (2007)Force unfolding kinetics of RNA using laser tweezers. II. Modeling experiments. Biophys. J. 92, 3010-21
• Tinoco, I., Jr., Li, P.T.X., and Bustamante, C. (2006) Determination of thermodynamics and kinetics of RNA reactions by force. Q. Rev. Biophys. 39, 325-360
• Li, P.T.X., Smith, S.B., Bustamante, C., and Tinoco, I., Jr. (2006) Probing the mechanical folding of TAR RNA by hopping, force-jump and force-clamp methods. Biophys. J. 90, 1-11
• Li, P.T.X., Bustamante, C., and Tinoco, I., Jr. (2006) Unusual mechanical stability of a minimal RNA kissing complex. Proc. Natl. Acad. Sci. U.S.A. 103, 7039-44
• Tinoco, I. Jr., Collin, D., Li, P.T.X. 2004. The effect of force on thermodynamics and kinetics: unfolding single RNA molecules. Biochem. Soc. Transactions 32: 757-60. 
• Li, P.T.X. & Gollnick, P. 2004. Characterization of a trp RNA-binding attenuation protein (TRAP) mutant with tryptophan independent RNA binding activity. J. Mol Biol. 335: 707-22. 
• Li, P.T.X. & Gollnick, P. 2002. Using hetero-11-mers composed of wild type and mutant subunits to study tryptophan binding to TRAP and its role in activating RNA binding. J. Biol. Chem. 277: 35567-35573 
• Li, P.T.X., Scott, D.J. & Gollnick, P. 2002. Creating hetero-11-mers composed of wild-type and mutant subunits to study RNA binding to TRAP J. Biol. Chem. 277: 11838-11844. 
• Chen, X., Antson, A.A., Yang, M., Li, P., Baumann, C., Dodson, E.J., Dodson, G.G. & Gollnick, P. 1999 Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus. J.Mol. Biol. 289: 1003-016.