Single Molecule Biophysics: Microscopy, Kinetics and Thermodynamics

Recent Papers in these Areas:

J. L. Fiore and D. J. Nesbitt, “An entropic origin of Mg+2–facilitated RNA folding,” Proc. Nat. Acad. Sci. 109, 2902-2907 (2012).

E. D. Holmstrom, J. L. Fiore and D. J. Nesbitt, “Thermodynamic Origins of Monovalent-Facilitated RNA Folding,” Biochemistry 51, 3732-3743 (2012).

E. D. Holmstrom, L. R. Fiegland, J. H. Hodak, and D. J. Nesbitt, “The Role of Counterion Valence and Size in GAAA Tetraloop–Receptor Docking/Undocking Kinetics”, J. Mol. Biol. (2012).

L. R. Fiegland, A. D. Garst, R. T. Batey, and D. J. Nesbitt, “Single-Molecule Studies of the Lysine Riboswitch Reveal Effector Dependent Conformational Dynamics of the Aptamer Domain,” Biochem. 51, 9223-9233, (2012).

J. L. Fiore and D. J . Nesbitt, “An RNA folding motif: GNRA tetraloop-receptor interactions,” Quart. Rev. . Biophys. 46, 223-264 (2013).

N. F. Dupuis, E. D. Holmstrom and D. J. Nesbitt, “Single molecule kinetics reveal cation promoted DNA duplex formation through ordering of single stranded helices,” Biophys. J. 105, 756-766, (2013).

 E. D. Holmstrom, N. F. Dupuis and D. J. Nesbitt, “Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics,” Biophys. J. 106, 220-231 (2014).

N. F. Dupuis, E. D. Holmstrom and D. J. Nesbitt, “Molecular crowding effects on single molecule RNA folding/unfolding thermodynamics and kinetics,” Proc. Nat. Acad. Sci, 111, 8464-8469, (2014).

E. D. Holmstrom and D. J. Nesbitt, “Single-molecule fluorescence resonance energy transfer studies of the human telomerase RNA psuedoknot: Temperature/urea dependent folding kinetics and thermodynamics,” J. Phys. Chem. B 118, 3853-3863, (2014).

E. D. Holmstrom, J. T. Polaski, R. T. Batey, and D. J. Nesbitt, “Single-molecule conformational dynamics of a biologically functional hydroxocobalamin riboswitch,” J. Am. Chem. Soc. 136, 16832-16843 (2014).

Y. Liu, E. Holmstrom, P. Yu, J. Wang, J. Zhang, M. A. Dyba, D. Chen, S. Lockett, D. J. Nesbitt, A. Ferre-D’Amare, R. Sousa, J. R. Stagno, and Y.-X. Wang, “Synthesis and applications of RNAs with position-selective labelling and mosaic composition,” Nature 522, 368-372  (2015).

E. D. Holmstrom, N. F. Dupuis, and D. J. Nesbitt, “Kinetic and thermodynamic origins of osmolyte-influenced nucleic acid folding,” J. Phys. Chem. B. (2015).

M. Vieweger, Holmstrom, E. D. , and Nesbitt, D. J. , Single-Molecule FRET Three Conformations for the tRNA-like Structure of Brome Mosaic Virus, BioPhysical Journal, vol. 109, no. 12, pp. 2625–2636, 2015.

E. D. Holmstrom and Nesbitt, D. J. , Biophysical Insights from Temperature-Dependent Single-Molecule Förster Resonance Energy Transfer, Annual Review of Physical Chemistry, vol. 67, 2016.

J. T. Polaski, Holmsrom, E. D. , Nesbitt, D. J. , and Batey, R. T. , Mechanistic Insights into Cofactor-Dependent Coupling of RNA Folding and mRNA Transcription/Translation by a Cobalamin Riboswitch, Cell Reports, vol. 15, no. 5, pp. 1100-1110, 2016.

A. Sengupta, Sung, H. , and Nesbitt, D. J. , Amino Acid Specific Effects on RNA Tertiary Interactions: Single Molecule Kinetic and Thermodynamic Studies, Physical Chemisty B, 2016.

M. Viewweger and Nesbitt, D. J. , SHAPE Probing the Three Conformational States in tRNA-like structures (TLS) Domain of Brome Mosaic Virus (BMV), Biophysical Journal, Submitted.