43. "De Novo Asymmetric Synthesis of Fridamycin E" Qian Chen, Michael Mulzer, Pei Shi, Penny J. Beuning, Geoffrey W. Coates, and George A. O’Doherty Organic Letters 13 6592-6595 (2011) http://dx.doi.org/10.1021/ol203041b
42. "A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase" Srinivas Somarowthu, Heather R. Brodkin, J. Alejandro D'Aquino, Dagmar Ringe, Mary Jo Ondrechen, Penny J. Beuning Biochemistry 50 9283–9295 (2011) http://dx.doi.org/10.1021/bi201089v
41. "Electron spin labeling reveals the highly dynamic N-terminal arms of the SOS mutagenesis protein UmuD" Jaylene N. Ollivierre, David E. Budil, and Penny J. Beuning Molecular BioSystems 7 3183-3186 (2011) dx.doi.org/10.1039/C1MB05334E
40. "Characterization of Escherichia coli UmuC Active Site Loops Identifies Variants that Confer UV Hypersensitivity" Lisa A. Hawver, Caitlin A. Gillooly, and Penny J. Beuning Journal of Bacteriology 193 5400-5411 (2011) dx.doi.org/10.1128/JB.05301-11
39. "Chapter 486 UmuC D Lesion Bypass DNA Polymerase V" Lisa A. Hawver and Penny J. Beuning; in Encyclopedia of Biological Chemistry 2nd edition W. J. Lennarz and M. D. Lane, Eds., Elsevier Science, in press. (encyclopedia chapter)
38. "Escherichia coli processivity clamp beta from DNA polymerase III is dynamic in solution" Jing Fang, John R. Engen, and Penny J. Beuning Biochemistry 50 5958-5968 (2011) dx.doi.org/10.1021/bi200580b
37. "Crystal Structure of Metal-Dependent Phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity" Gye-Won Han, Jaejo Ko, Carol L. Farr, Marc C. Deller, Qingping Xu, Hsiu-Ju Chiu, Mitchell D. Miller, Jana Sefcikova, Srinivas Somarowthu, Penny J. Beuning, Marc-Andre Elsliger, Ashley Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson, and Mary Jo Ondrechen Proteins: Structure, Function, and Bioinformatics 79 2146-2160 (2011) dx.doi.org/10.1002/prot.23035
36. "Discrimination against the Cytosine Analog tC by Escherichia coli DNA Polymerase IV DinB" Jason M. Walsh, Imenne Bouamaied, Tom Brown, L. Marcus Wilhelmsson, and Penny J. Beuning Journal of Molecular Biology 409 89-100 (2011) dx.doi.org/10.1016/j.jmb.2011.03.069
35. "False EX1 signatures caused by sample carryover during HXMS analyses" Jing Fang, Kasper D. Rand, Penny J. Beuning, and John R. Engen International Journal of Mass Spectrometry 302 19-25 (2011) dx.doi.org/10.1016/j.ijms.2010.06.039
34. "Escherichia coli Y Family DNA Polymerases" Jason M. Walsh, Lisa A. Hawver, and Penny J. Beuning Frontiers in Bioscience 16 3164-3182 (2011) dx.doi.org/10.2741/3904
33. "The dimeric SOS mutagenesis protein UmuD is active as a monomer" Jaylene N. Ollivierre, Jacquelyn L. Sikora, and Penny J. Beuning Journal of Biological Chemistry 286 3607-3617 (2011) dx.doi.org/10.1074/jbc.M110.167254
32. "Polymerase switching in response to DNA damage" Jaylene N. Ollivierre, Michelle C. Silva, Jana Sefcikova, and Penny J. Beuning in Biophysics of DNA-Protein Interactions: from single molecules to biological systems M.C. Williams and L. J. Maher, III, Eds., Springer, New York, NY (2010).
31. "The roles of UmuD in regulating mutagenesis" Jaylene N. Ollivierre, Jing Fang, and Penny J. Beuning, Journal of Nucleic Acids Article ID 947680; 12 pages; doi:10.4061/2010/947680 (2010) dx.doi.org/10.4061/2010/947680
30. "Conformational dynamics of the Escherichia coli polymerase manager proteins UmuD and UmuD' " Jing Fang, Kasper D. Rand, Michelle C. Silva, Thomas E. Wales, John R. Engen, and Penny J. Beuning Journal of Molecular Biology 398 40-53 (2010) dx.doi.org/10.1016/j.jmb.2010.02.040
29. "Signal Transduction in the Escherichia coli SOS Response" James J. Foti, Lyle A. Simmons, Penny J. Beuning, and Graham C. Walker in Handbook of Cell Signaling Second Ed. R.A. Bradshaw and E.A. Dennis, Eds., Chapter 258, pp. 2127-2136, Elsevier Science, San Diego, CA (2009).
28. "Song: SOS" Sharotka M. Simon, Lauren S. Waters, Daniel F. Jarosz, and Penny J. Beuning Biochemistry and Molecular Biology Education 37 316 (2009) dx.doi.org/10.1002/bmb.20305
27. "Characterization of Novel Alleles of the Escherichia coli umuDC genes Identifies Additional Interaction Sites of UmuC with the Beta Clamp" Penny J. Beuning, Sarah Chan, Lauren S. Waters, Haripriya Addepalli, Jaylene N. Ollivierre, and Graham C. Walker Journal of Bacteriology 191 5910-5920 (2009) dx.doi.org/10.1128/JB.00292-09
26. "Steric Gate Variants of UmuC Confer UV Hypersensitivity on Escherichia coli" Brenna W. Shurtleff, Jaylene N. Ollivierre, Mohammad Tehrani, Graham C. Walker, and Penny J. Beuning Journal of Bacteriology 191 4815-4823 (2009) dx.doi.org/10.1128/JB.01742-08
25. "Distinct Double- and Single-Stranded DNA Binding of E. coli Replicative DNA Polymerase III Alpha Subunit" Micah J. McCauley, Leila Shokri, Jana Sefcikova, Ceslovas Venclovas, Penny J. Beuning, and Mark C. Williams ACS Chemical Biology 3 577-587 (2008) dx.doi.org/10.1021/cb8001107
24. "Y-Family DNA Polymerases in Escherichia coli" Daniel F. Jarosz, Penny J. Beuning, Susan E. Cohen, and Graham C. Walker Trends in Microbiology 15 70-77 (2007) dx.doi.org/10.1016/j.tim.2006.12.004
23. "Single DNA molecule stretching experiments provide an efficient method for determining the activity of drugs that target the HIV-1 nucleocapsid protein" Margareta Cruceanu, Andrew G. Stephen, Penny J. Beuning, Robert J. Gorelick, Robert J. Fisher, and Mark C. Williams, Analytical Biochemistry 358 159-170 (2006) dx.doi.org/10.1016/j.ab.2006.08.037
22. "A Non-Cleavable UmuD Variant that Acts as a UmuD' Mimic" Penny J. Beuning, Sharotka M. Simon, Adam Zemla, Daniel Barsky, and Graham C. Walker, Journal of Biological Chemistry 281 9633-9640 (2006) dx.doi.org/10.1074/jbc.M511101200
21. "Two Processivity Clamp Interactions Differentially Alter the Dual Activities of UmuC" Penny J. Beuning, Dorota Sawicka, Daniel Barsky, and Graham C. Walker, Molecular Microbiology 59 460-474 (2006) dx.doi.org/10.1111/j.1365-2958.2005.04959.x
20. "Characterization of E. coli translesion synthesis polymerases and their accessory factors" Penny J. Beuning, Sharotka M. Simon, Veronica G. Godoy, Daniel F. Jarosz, and Graham C. Walker, Methods in Enzymology 408 318-340 (2006) dx.doi.org/10.1016/S0076-6879(06)08020-7
19. "Gene Expression in Bacterial Systems: The LexA Regulatory System" in Encyclopedia of Biological Chemistry Vol 2., Veronica G. Godoy, Penny J. Beuning and Graham C. Walker; W. J. Lennarz and M. D. Lane, Eds., Academic Press/Elsevier Science, San Diego, CA. pp. 546-550, (2004) (encyclopedia chapter)
18. "Signal Transduction in the SOS Response" in Handbook of Cellular Signaling, Volume 3, Penny J. Beuning and Graham C. Walker; Al Fornace, Ed. Chapter 299, pp. 185-189. Elsevier Science, San Diego, CA (2003) (book chapter)
17. "An isolated class II aminoacyl-tRNA synthetase insertion domain is functional in amino acid editing" Fai-Chu Wong, Penny J. Beuning, Carmen Silvers, and Karin Musier-Forsyth, Journal of Biological Chemistry 278 52857-52864 (2003) dx.doi.org/10.1074/jbc.M309627200
16. "Introducing the National Postdoctoral Association (NPA): A Resource and A Voice for Postdoctoral Scholars." Penny J. Beuning and Amy J. Reese, AWIS Magazine 32 27-29 (2003).
15. "Functional role of the prokaryotic proline-tRNA synthetase insertion domain in amino acid editing." Fai-Chu Wong*, Penny J. Beuning*, Maria C. Nagan, Kiyotaka Shiba, and Karin Musier-Forsyth, Biochemistry 41 7108-7115 (2002) dx.doi.org/10.1021/bi012178j
14. "Efficient Aminoacylation of the tRNAAla Acceptor Stem: Dependence on 2:71 Base Pair" Penny J. Beuning*, Maria C. Nagan*, Christopher J. Cramer, Karin Musier-Forsyth, Josep-Lluis Gepi, and Donald Bashford, RNA 8 659-670 (2002).
13. "Amino acid activation of a dual-specificity tRNA synthetase is independent of tRNA" Richard S. Lipman*, Penny J. Beuning*, Karin Musier-Forsyth and Ya-Ming Hou, Journal of Molecular Biology 316 421-427 (2002) dx.doi.org/10.1006/jmbi.2001.5373
12. "Alanine-tRNA synthetase recognition of wild-type microhelixAla versus a C1:G72 variant: An NMR and molecular dynamics analysis" Deborah A. Kallick, Maria C. Nagan, Penny J. Beuning, Stephanie Kerimo, Michael R. Tessmer, Christopher J. Cramer, and Karin Musier-Forsyth, Journal of Physical Chemistry B 106 8878-8884 (2002) dx.doi.org/10.1021/jp020956r
11. "Species-Specific Differences in Amino Acid Editing by Class II Prolyl-tRNA Synthetase" Penny J. Beuning and Karin Musier-Forsyth, Journal of Biological Chemistry 276 30779-30785 (2001) dx.doi.org/10.1074/jbc.M104761200
10. "Hydrolytic Editing by a Class II Aminoacyl-tRNA Synthetase" Penny Beuning and Karin Musier-Forsyth Proceedings of the National Academy of Sciences 97 8916-8920 (2000)dx.doi.org/10.1073/pnas.97.16.8916
9. "Importance of Discriminator-Base Stacking Interactions: Molecular Dynamics Analysis of A73 MicrohelixAla Variants" Maria C. Nagan, Penny Beuning, Karin Musier-Forsyth, and Christopher J. Cramer Nucleic Acids Research 28 2527-2534 (2000)dx.doi.org/10.1093/nar/28.13.2527
8. "Role of Zinc Ion in Translational Accuracy Becomes Crystal Clear" Karin Musier-Forsyth and Penny J. Beuning Nature Structural Biology 7 435-436 (2000) (News and Views)
7. "Transfer RNA Recognition by Aminoacyl-tRNA Synthetases" Karin Musier-Forsyth and Penny Beuning Biopolymers 52 1-28 (1999) (Review) dx.doi.org/10.1002/(SICI)1097-0282(1999)52:1<1::AID-BIP1>3.0.CO;2-W
6. "Increasing Retention and Improving the Climate for Women in Chemistry" Penny Beuning and Susan Page 1999 CIC WISE Best Practices Guidebook: Mentoring Programs Edited by Jane Zimmer Daniels 17-22 (1999)
5. "Identification of Discriminator Base Atomic Groups That Modulate the Alanine Aminoacylation Reaction" Abbey Fischer, Penny Beuning, and Karin Musier-Forsyth Journal of Biological Chemistry 274 37093-37096 (1999) dx.doi.org/10.1074/jbc.274.52.37093
4. "Sequence-Dependent Conformational Differences of Small RNAs Revealed by Native Gel Electrophoresis" Penny Beuning, Michael Tessmer, Christoph Baumann, Deborah Kallick and Karin Musier-Forsyth Analytical Biochemistry 273 284-290 (1999) dx.doi.org/10.1006/abio.1999.4223
3. "Subtle Functional Interactions in the RNA Minor Groove at a Nonessential Base Pair" Barry S. Henderson, Penny J. Beuning, J-P. Shi, Rolf Bald, Jens Peter Fuerste, Volker A. Erdmann, Karin Musier-Forsyth, and Paul Schimmel Journal of the American Chemical Society 120 9110-9111 (1998) dx.doi.org/10.1021/ja9809152
2. "Specific Atomic Groups and RNA Helix Geometry in Acceptor Stem Recognition by a tRNA Synthetase" Penny J. Beuning, Fan Yang, Paul Schimmel, and Karin Musier-Forsyth Proceedings of the National Academy of Sciences 94 10150-10154 (1997) >
1. "Atomic Group 'Mutagenesis' Reveals Major Groove Fine Interactions of a tRNA Synthetase with an RNA Helix" Penny J. Beuning, Miriam Gulotta, and Karin Musier-Forsyth Journal of the American Chemical Society 119 8397-8402 (1997) dx.doi.org/10.1021/ja971020c