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Julia Widom

Julia Widom profile picture
  • Affiliation: faculty
  • Title: Assistant Professor
  • Phone: 541-346-4670
  • Office: 139 Klamath Hall
  • Affiliated Departments: Institute of Molecular Biology
  • Interests: RNA, ultrafast spectroscopy, single-molecule microscopy
  • Curriculum Vitae

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 will use a variety of biophysical techniques, centered around ultrafast and single-molecule spectroscopy, to probe the structures and dynamics of systems ranging from isolated RNAs to large RNA-protein complexes. We will also take advantage of the inherent folding ability of RNA to make nanostructures that position chromophores in specific locations, allowing us to characterize the optical properties that arise from specific chromophore arrangements. RNA is an excellent platform for such studies, because its structure is encoded in its sequence and can therefore be readily programmed and manipulated.

Publications

1.     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,” in press at Mol. Cell.

2.     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.

3.     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.

4.     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.

5.     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. B2015, 119, 7985-7993.

6.     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.

7.     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.

8.     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.

9.     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.

10.  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.

11.  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.

12.  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.   

13.  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.

14.  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.

15.  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.

16.  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.

17.  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.

18.  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.