Julia Widom

Julia Widom grew up in Pittsburgh, PA and earned her B.A. in Chemistry from Northwestern University in 2009. She did her graduate work at the University of Oregon in the lab of Andy Marcus, earning her Ph.D. in 2013. Her research utilized fluorescence-detected multidimensional spectroscopy to study the conformations of porphyrins and nucleic acids. From 2014 to 2018, she worked as a postdoc in the lab of Nils Walter at the University of Michigan, where she used single-molecule fluorescence methods to study RNA folding. She returned to UO as a faculty member in the Physical Chemistry division in September, 2018. Her lab works at the interface of physical chemistry and molecular biology, using ultrafast and single-molecule spectroscopy to study RNA structure and dynamics. She is a member of the Oregon Center for Optical, Molecular and Quantum Science and an associate member of the Institute for Molecular Biology. In her free time, she enjoys rock climbing, hiking and baking fancy cakes.

Julia’s CV

Publications 

† These authors contributed equally to this work.

  1. Widom, J. R. “Fluorescence-detected circular dichroism for analysis of nucleic acids: A practical guide and review”. 2024 Invited chapter for Springer Nature volume “Nucleic Acid Photophysics and Photochemistry”.
  2. Hoeher, J. E.; Sande, N. E.; Widom, J. R.* “Probing and perturbing riboswitch folding using a fluorescent base analogue”. Photochem. Photobiol., 2023, 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, 72, 1457-1469.
  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, 541-558.
  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,” Meth. 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(40), 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(1), 487-520.