Biophysics of Conformational Folding at the Single Molecule Level: RNA, DNA, Riboswitches, and Ribozymes
 
David J. Nesbitt, JILA/Department of Chemistry/Department of Physics

Biophysics, single molecule microscopy, FRET, time correlated single photon counting, nucleoproteins, CRISPR/CAS9, riboswitches, high pressure

The ability to “see” single biomolecules with laser microscopy has led to a revolution in research opportunities for chemistry, physics and molecular biology. This project takes advantage of how we can combine optical microscopy, single photon counting, and laser fluorescence methods to probe/measure the folding of single nucleic acid molecules (e.g., DNA and RNA) in real time. As JILA is located in Boulder, we are particularly interested in RNA based biophysical systems, but we are also exploring protein-nucleic acid systems as well. Unique capabilities in our group include the ability to heat single biomolecules with IR laser light to study T dependent kinetics and thermodynamics relevant to evolution of thermophilic species. We have also recently developed powerful new capabilities for studying single molecule biophysics at extreme pressures (4000 atm), which is proving to be quite relevant for understanding evolution of marine life in the very deepest regions of the ocean floor. As one of several other examples explored in the group, we are interested in the physics of G-quadruplex folding, the conformational kinetics of Cas9-CRISPR ribonucleoproteins, and the effects of chirality on biophysics of folding.

3 Recent Publications:
H.-L. Sung and D. J. Nesbitt, “Ligand-Dependent Volumetric Characterization of Manganese Riboswitch Folding: A High-Pressure Single-Molecule Kinetic Study”, J. Phys. Chem. B, (2022) https://doi-org.colorado.idm.oclc.org/10.1021/acs.jpcb.2c06579.

H-L Sung and D. J. Nesbitt, “Synergism in the Molecular Crowding of Ligand-Induced Riboswitch Folding: Kinetic/Thermodynamic Insights from Single Molecule FRET Spectroscopy”, J. Phys. Chem. 126, 6419–6427 (2022) https://doi-org.colorado.idm.oclc.org/10.1021/acs.jpcb.2c03507.

A. M. Menendez and D. J. Nesbitt, “Ionic cooperation between lysine and potassium in the lysine riboswitch: single molecule kinetic and thermodynamic studies”, J. Phys. Chem. B (2023) doi.org/10.1021/acs.jpcb.3c00245.