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Julia R. Widom, Ph.D. - Publications

Affiliations: 
2013 Chemistry and Biochemistry University of Oregon, Eugene, OR, United States 
Area:
DNA transcription and replication
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Widom JR, Rai V, Rohlman CE, Walter NG. Versatile transcription control based on reversible dCas9 binding. Rna (New York, N.Y.). PMID 31320398 DOI: 10.1261/Rna.071613.119  0.373
2018 Widom JR, Nedialkov YA, Rai V, Hayes RL, Brooks CL, Artsimovitch I, Walter NG. Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing. Molecular Cell. 72: 541-552.e6. PMID 30388413 DOI: 10.1016/J.Molcel.2018.08.046  0.333
2018 Kringle L, Sawaya NPD, Widom J, Adams C, Raymer MG, Aspuru-Guzik A, Marcus AH. Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA. The Journal of Chemical Physics. 148: 085101. PMID 29495791 DOI: 10.1063/1.5020084  0.449
2018 Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chemical Reviews. PMID 29363314 DOI: 10.1021/Acs.Chemrev.7B00519  0.362
2017 Daher M, Widom JR, Tay W, Walter NG. Soft interactions with model crowders and non-canonical interactions with cellular proteins stabilize RNA folding. Journal of Molecular Biology. PMID 29128594 DOI: 10.1016/J.Jmb.2017.10.030  0.339
2015 Kahlscheuer ML, Widom J, Walter NG. Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines. Methods in Enzymology. 558: 539-70. PMID 26068753 DOI: 10.1016/Bs.Mie.2015.01.009  0.384
2015 Saif M, Widom JR, Xu S, Abbey ER, Liu SY, Marcus AH. Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives. The Journal of Physical Chemistry. B. 119: 7985-93. PMID 26000556 DOI: 10.1021/Acs.Jpcb.5B03485  0.386
2014 Karki KJ, Widom JR, Seibt J, Moody I, Lonergan MC, Pullerits T, Marcus AH. Coherent two-dimensional photocurrent spectroscopy in a PbS quantum dot photocell. Nature Communications. 5: 5869. PMID 25519819 DOI: 10.1038/Ncomms6869  0.304
2014 Widom JR, Dhakal S, Heinicke LA, Walter NG. Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Archives of Toxicology. 88: 1965-85. PMID 25212907 DOI: 10.1007/S00204-014-1357-9  0.33
2014 Saif M, Widom JR, Xu S, Liu S, Marcus AH. Electronic Transition Moments of 1,3,2-Benzodiazaboroline (‘External’ Bn Indole) and ‘Fused’ Bn Indole, Containing the 1,2-Dihydro-1,2-Azaborine Core Biophysical Journal. 106: 206a. DOI: 10.1016/J.Bpj.2013.11.1208  0.381
2013 Widom JR, Johnson NP, von Hippel PH, Marcus AH. Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS). New Journal of Physics. 15. PMID 24223491 DOI: 10.1088/1367-2630/15/2/025028  0.571
2013 Raymer MG, Marcus AH, Widom JR, Vitullo DL. Entangled photon-pair two-dimensional fluorescence spectroscopy (EPP-2DFS). The Journal of Physical Chemistry. B. 117: 15559-75. PMID 24047447 DOI: 10.1021/Jp405829N  0.359
2013 Widom JR, Lee W, Perdomo-Ortiz A, Rappoport D, Molinski TF, Aspuru-Guzik A, Marcus AH. Temperature-dependent conformations of a membrane supported zinc porphyrin tweezer by 2D fluorescence spectroscopy. The Journal of Physical Chemistry. A. 117: 6171-84. PMID 23480874 DOI: 10.1021/Jp400394Z  0.349
2013 Widom JR, Rappoport D, Perdomo-Ortiz A, Thomsen H, Johnson NP, von Hippel PH, Aspuru-Guzik A, Marcus AH. Electronic transition moments of 6-methyl isoxanthopterin--a fluorescent analogue of the nucleic acid base guanine. Nucleic Acids Research. 41: 995-1004. PMID 23185042 DOI: 10.1093/Nar/Gks1148  0.563
2013 Widom JR, Perdomo-Ortiz A, Lee W, Johnson NP, Hippel PHv, Aspuru-Guzik A, Marcus AH. Determining the Conformations of Porphyrin Dimers and Dinucleotide-Substituted DNA Constructs by 2-Dimensional Fluorescence Spectroscopy Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.2361  0.438
2012 Perdomo-Ortiz A, Widom JR, Lott GA, Aspuru-Guzik A, Marcus AH. Conformation and electronic population transfer in membrane-supported self-assembled porphyrin dimers by 2D fluorescence spectroscopy. The Journal of Physical Chemistry. B. 116: 10757-70. PMID 22882118 DOI: 10.1021/Jp305916X  0.342
2011 Lott GA, Perdomo-Ortiz A, Utterback JK, Widom JR, Aspuru-Guzik A, Marcus AH. Conformation of self-assembled porphyrin dimers in liposome vesicles by phase-modulation 2D fluorescence spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 108: 16521-6. PMID 21940499 DOI: 10.1073/Pnas.1017308108  0.373
2004 Thåström A, Bingham LM, Widom J. Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning. Journal of Molecular Biology. 338: 695-709. PMID 15099738 DOI: 10.1016/J.Jmb.2004.03.032  0.403
2004 Thåström A, Lowary PT, Widom J. Measurement of histone-DNA interaction free energy in nucleosomes. Methods (San Diego, Calif.). 33: 33-44. PMID 15039085 DOI: 10.1016/J.Ymeth.2003.10.018  0.426
2002 Anderson JD, Thåström A, Widom J. Spontaneous access of proteins to buried nucleosomal DNA target sites occurs via a mechanism that is distinct from nucleosome translocation. Molecular and Cellular Biology. 22: 7147-57. PMID 12242292 DOI: 10.1128/Mcb.22.20.7147-7157.2002  0.434
2001 Anderson JD, Widom J. Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Molecular and Cellular Biology. 21: 3830-9. PMID 11340174 DOI: 10.1128/Mcb.21.11.3830-3839.2001  0.395
2001 Anderson JD, Lowary PT, Widom J. Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites. Journal of Molecular Biology. 307: 977-85. PMID 11286549 DOI: 10.1006/Jmbi.2001.4528  0.4
2000 Protacio RU, Li G, Lowary PT, Widom J. Effects of histone tail domains on the rate of transcriptional elongation through a nucleosome. Molecular and Cellular Biology. 20: 8866-78. PMID 11073987 DOI: 10.1128/Mcb.20.23.8866-8878.2000  0.333
2000 Polach KJ, Lowary PT, Widom J. Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes. Journal of Molecular Biology. 298: 211-23. PMID 10764592 DOI: 10.1006/Jmbi.2000.3644  0.394
2000 Anderson JD, Widom J. Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. Journal of Molecular Biology. 296: 979-87. PMID 10686097 DOI: 10.1006/Jmbi.2000.3531  0.418
1999 Thåström A, Lowary PT, Widlund HR, Cao H, Kubista M, Widom J. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. Journal of Molecular Biology. 288: 213-29. PMID 10329138 DOI: 10.1006/Jmbi.1999.2686  0.394
1998 Lowary PT, Widom J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. Journal of Molecular Biology. 276: 19-42. PMID 9514715 DOI: 10.1006/Jmbi.1997.1494  0.398
1997 Protacio RU, Polach KJ, Widom J. Coupled-enzymatic assays for the rate and mechanism of DNA site exposure in a nucleosome. Journal of Molecular Biology. 274: 708-21. PMID 9405153 DOI: 10.1006/Jmbi.1997.1440  0.412
1996 Polach KJ, Widom J. A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites Journal of Molecular Biology. 258: 800-812. PMID 8637011 DOI: 10.1006/Jmbi.1996.0288  0.356
1996 Protacio RU, Widom J. Nucleosome transcription studied in a real-time synchronous system: test of the lexosome model and direct measurement of effects due to histone octamer. Journal of Molecular Biology. 256: 458-472. PMID 8604131 DOI: 10.1006/Jmbi.1996.0101  0.419
1995 Polach KJ, Widom J. Mechanism of Protein Access to Specific DNA Sequences in Chromatin: A Dynamic Equilibrium Model for Gene Regulation Journal of Molecular Biology. 254: 130-149. PMID 7490738 DOI: 10.1006/Jmbi.1995.0606  0.426
1992 Godde JS, Widom J. Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length. Journal of Molecular Biology. 226: 1009-1025. PMID 1518041 DOI: 10.1016/0022-2836(92)91049-U  0.367
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