Profile picture of Julia Widom

Julia Widom

Assistant Professor
Division of Physical Chemistry
Chemistry and Biochemistry, OMQ
jwidom@uoregon.edu
Phone: 541-346-4670
Office: 139 Klamath Hall
Research Interests: RNA, ultrafast spectroscopy, single-molecule microscopy
Lab Website: https://blogs.uoregon.edu/widomlab/

Education

B.A. in Chemistry, Northwestern University, 2009

Ph.D. in Physical Chemistry, University of Oregon, 2013

Postdoctoral Research Fellow, University of Michigan, 2014-2018

Research

My research focuses on RNA, which performs a plethora of different functions in the cell by folding into specific structures and, often, interconverting between different structures. My lab uses a variety of biophysical techniques, centered around spectroscopy and single-molecule microscopy, to probe the structures and dynamics of systems ranging from isolated RNAs to large RNA-protein complexes. Our current research focuses on RNAs that regulate gene expression through their interactions with proteins and metabolites. We also investigate very short RNAs as model systems, uncovering how the spectroscopic signals that we use to study more complex systems depend on the fine details of RNA structure.

Publications

  1. Widom, J. R. "Fluorescence-detected circular dichroism for analysis of nucleic acids: A practical guide and review". Invited chapter for Springer Nature volume "Nucleic Acid Photophysics and Photochemistry", 2024.
  2. Hoeher, J. E.; Sande, N. E.; Widom, J. R.* "Probing and perturbing riboswitch folding using a fluorescent base analogue". Photochem. Photobiol., 2024, 100, 419-433.
  3. Wonderlick, D. R.; Widom, J. R.; Harms, M. J. “Disentangling contact and ensemble epistasis in a riboswitch”. Biophys. J., 2023, 122, 1600-1612.
  4. Widom, J. R.*, Hoeher, J. E. “Base-Stacking Heterogeneity in RNA Resolved by Fluorescence-Detected Circular Dichroism Spectroscopy”. J. Phys. Chem. Lett., 2022, 13, 8010-8018.
  5. Yadav, R.; Widom, J. R.; Chauvier, A.; Walter, N. G. “An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch”. Nat. Commun., 2022, 13, 207.
  6. Widom, J. R.*; Rai, V.; Rohlman, C. E.; Walter, N. G.* "Versatile Transcription Control based on Reversible dCas9 Binding," RNA, 2019, 25, 1457-1469.1.
  7. Widom, J. R.; Nedialkov, Y. A.; Rai, V.; Hayes, R. L.; Brooks III, C. L.; Artsimovitch, I. A.; Walter, N. G. “Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing,” Mol. Cell, 2018, 72, 541-555.
  8. †Ray, S. R.; †Widom, J. R.; Walter, N. G. "Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World," Invited review for "RNA: From Single Molecule to Medicine" special issue at Chem. Rev., 2018, 118, 4120-4155.
  9. Kringle, L.; Sawaya, N.; Widom, J. R.; Adams, C.; Raymer, M. G.; Aspuru-Guzik, A.; Marcus, A. H. "Temperature-Dependent Vibronic Coupling of Cy3 Dimers in Double-Stranded DNA," Featured cover article in J. Chem. Phys., 2018, 148, 085101.
  10. Daher, M.; Widom, J. R.; Tay, W.; Walter, N. G. “Soft Interactions with Model Crowders and Non-Canonical Interactions with Cellular Proteins Drive RNA Folding”, J. Mol. Biol., 2018, 430, 509-523.
  11. Saif, M.; Widom, J. R.; Xu, S.; Abbey, E. R.; Liu, S.; Marcus, A. H. “Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives,” J. Phys. Chem. B, 2015, 119, 7985-7993.
  12.     Kahlscheuer, M. L.; Widom, J. R.; Walter, N. G. “Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines,” Invited chapter for volume “Structures of Large RNA Molecules and their Complexes,” Method. Enzymol., 2015, 558, 539-570.
  13.   Le, H. V.; Hawker, D. D.; Wu, R.; Doud, E.; Widom, J. R., Sanishvili, R.; Liu, D.; Kelleher, N. L.; Silverman, R. B. “Design and Mechanism of Tetrahydrothiophene-based GABA Aminotransferase Inactivators,” J. Am. Chem. Soc., 2015, 137, 4525-4533.
  14.   †Karki, K. J.; †Widom, J. R.; Seibt, J.; Moody, I.; Lonergan, M C.; Pullerits, T.; Marcus, A. H. “Coherent Two-Dimensional Photocurrent Spectroscopy in a PbS Quantum Dot Photocell,” Nat. Commun., 2015, 5, 5869-1-7.
  15.    Widom, J. R.; Dhakal, S.; Heinicke, L.; Walter, N. G. “Single-Molecule Tools for Enzymology, Structural Biology, Systems Biology and Nanotechnology: an Update,” Invited review, Arch. Toxicol., 2014, 88, 1965-1985.
  16.   Raymer, M. R.; Marcus, A. H.; Widom, J. R.; Vitullo, D. “Entangled Photon-Pair Two Dimensional Fluorescence Spectroscopy (EPP-2DFS),” Invited research article for Prof. Michael D. Fayer Festschrift special issue, J. Phys. Chem. B, 2013, 117, 15559-15575.
  17.  Karki, K. J.; Torbjornsson, M.; Widom, J. R.; Marcus, A. H.; Pullerits, T. “Digital Cavities and their Potential Applications,” J. Instrum., 2013, 8, T05005-1-12.
  18.  Widom, J. R.; Perdomo-Ortiz, A.; Lee, W.; Rappoport, D.; Molinski, T. F.; Aspuru-Guzik, A.; Marcus, A. H. “Temperature-Dependent Conformations of a Membrane Supported ‘Zinc Porphyrin Tweezer’ by 2D Fluorescence Spectroscopy,” Invited research article for Prof. John C. Wright Festschrift special issue. J. Phys. Chem. A., 2013, 117, 6171-6184.   
  19. Widom, J. R.; Johnson, N. P.; von Hippel, P. H.; Marcus, A. H. “Solution Conformation of 2-Aminopurine (2-AP) Dinucleotide by Ultraviolet 2D Fluorescence Spectroscopy (UV-2D FS),” Invited research article for special issue on 2D optical coherence spectroscopy, New J. Phys., 2013, 15, 025028-1-16.
  20. Widom, J. R.; Rappoport, D.; Perdomo-Ortiz, A.; Thomsen, H.; Johnson, N. P.; von Hippel, P. H.; Aspuru-Guzik, A.; Marcus, A. H. “Electronic Transition Moments of 6-Methyl Isoxanthopterin – a Fluorescent Analogue of the Nucleic Acid Base Guanine,” Nucleic Acids Res., 2013, 41, 995-1004.
  21. Sanders, J. N.; Saikin, S. K.; Mostame, S.; Andrade, X.; Widom, J. R.; Marcus, A. H.; Aspuru-Guzik, A. “Compressed Sensing for Multidimensional Spectroscopy Experiments,”  J. Phys. Chem. Lett., 2012, 3, 2697-2702.
  22. †Perdomo-Ortiz, A.; †Widom, J. R.; Lott, G. A.; Aspuru-Guzik, A.; Marcus, A. H. “Conformation and Electronic Population Transfer in Membrane-Supported Self-Assembled Porphyrin Dimers by 2D Fluorescence Spectroscopy,”  J. Phys. Chem. B, 2012, 116, 10757-10770.
  23. Lott, G. A.; Perdomo-Ortiz, A.; Utterback, J. K.; Widom, J. R.; Aspuru-Guzik, A.; Marcus, A. H. “Conformation of Self-Assembled Porphyrin Dimers in Liposome Vesicles by Phase-Modulation 2D Fluorescence Spectroscopy,”  Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 16521-16526.
  24. Wang, C.; Widom, J.; Petronijevic, F.; Burnett, J. C.; Nuss, J. E.; Bavari, S.; Gussio, R.; Wipf, P. “Synthesis and Biological Evaluation of Inhibitors of Botulinum Neurotoxin Metalloprotease,” Heterocycles, 2009, 79, 487-520.