Google scholar profile: https://scholar.google.com/citations?user=auHkDbsAAAAJ&hl=en

Book: “Teach Better, Save Time, and Have More Fun: A Guide to Teaching and Mentoring in Science”
Penny J. Beuning, Dave Z. Besson and Scott A. Snyder with an annotated bibliography by Ingrid DeVries Salgado, ISBN 9780963350497 (2014) Free download
Note that this work may not be quoted or reproduced without the permission of the authors or Research Corporation for Science Advancement.
To request a hard copy, contact Prof. Beuning.
Interactive on-line version: https://teachbettersavetime.wordpress.com/

84. “Jettison-MS of Nucleic Acid Species” Poguang Wang, Gunjan L. Shah, Heather J. Landau, Michael E. Coulter, Christopher A. Walsh, Elisabeth Roider, Caitlin S. Kramer, Penny J. Beuning and Roger W. Giese Journal of the American Society for Mass Spectrometry (2020) accepted https://pubs.acs.org/doi/10.1021/jasms.0c00084

83. “Probing remote residues important for catalysis in Escherichia coli Ornithine Transcarbamoylase” Lisa Ngu, Jenifer N. Winters, Kien Nguyen, Kevin E. Ramos, Nicholas A. DeLateur, Lee Makowski, Paul C. Whitford, Mary Jo Ondrechen, and Penny J. Beuning PLoS One 15(2):e0228487 (2020) https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228487

82. “Mammalian DNA Polymerase Kappa Activity and Specificity” Hannah R. Stern, Jana Sefcikova, Victoria E. Chaparro, and Penny J. Beuning Molecules 24 2805 (2019) https://doi.org/10.3390/molecules24152805.

81. “Dynamics of the E. coli β clamp dimer interface and its influence on DNA loading” Bilyana N. Koleva, Hatice Gokcan, Alessandro A. Rizzo, Socheata Lim, Kevin Jeanne Dit Fouque, Angelina Choy, Melissa L. Liriano, Francisco Fernandez-Lima, Dmitry M. Korzhnev, G. Andrés Cisneros, and Penny J. Beuning Biophysical Journal 117 587-601 (2019) https://doi.org/10.1016/j.bpj.2019.06.035.

80. “Engineering polymerases for new functions” Timothy A. Coulther, Hannah R. Stern, and Penny J. Beuning Trends in Biotechnology (2019) https://doi.org/10.1016/j.tibtech.2019.03.011.

79. “Site-Specific Reversible Protein and Peptide Modification: Transglutaminase-Catalyzed Glutamine Conjugation and Bioorthogonal Light-Mediated Removal.” Kevin R. Moulton, Amissi Sadiki, Bilyana N. Koleva, Lincoln J. Ombelets, Tina H. Tran, Shanshan Liu, Bryan Wang, Hongyan Chen, Emily Micheloni, Penny J. Beuning, George A. O’Doherty, and Zhaohui Sunny Zhou Bioconjugate Chemistry 30 1617-1621 (2019) https://doi.org/10.1021/acs.bioconjchem.9b00145.

78. “The Response of Escherichia coli to the Alkylating Agents Chloroacetaldehyde and Styrene Oxide” Mark M. Muenter, Ariel Aiken, Jadesola Akanji, Samir Baig, Sirine Bellou, Alyssa Carlson, Charles Conway, Courtney M. Cowell, Nicholas A. DeLateur, Alexis Hester, Christopher Joshi, Caitlin Kramer, Becky Leifer, Emma Nash, Macee Qi, Meghan Travers, Kelly C. Wong, Man Hu, Na Gou, Roger W. Giese, April Z. Gu, Penny J. Beuning Mutation Research – Genetic Toxicology and Environmental Mutagenesis  840 1-10 (2019) https://doi.org/10.1016/j.mrgentox.2019.02.001.

77. “Characterization of nine cancer-associated variants in human DNA polymerase κ” Nicole M. Antczak, Alice R. Walker, Hannah R. Stern, Emmett M. Leddin, Timothy A. Coulther, Carl Palad, Rebecca Swett, G. Andrés Cisneros, and Penny J. Beuning Chemical Research in Toxicology 31 697-711 (2018) https://doi.org/10.1021/acs.chemrestox.8b00055.

76. “Functional classification of protein structures by local structure matching in graph representation” Caitlyn L. Mills, Rohan Garg, Joslynn S. Lee, Liang Tian, Alexandru Suciu, Gene Cooperman, Penny J. Beuning, and Mary Jo Ondrechen Protein Science  27 1125-1135 (2018) https://doi.org/10.1002/pro.3416.

75. “A practical synthesis of glycinamide ribonucleotide” Debarpita Ray, Penny J. Beuning, Mary Jo Ondrechen, and George O’Doherty Heterocycles 97 (2018) http://dx.doi.org/10.3987/COM-18-S(T)50

74. “Role of Active Site and Distal Residues in E. coli DNA Polymerase III Alpha” Ramya Parasuram, Timothy A. Coulther, Judith M. Hollander, Elise Keston-Smith, Mary Jo Ondrechen, and Penny J. Beuning Biochemistry 57 1063-1072. (2018) http://dx.doi.org/10.1021/acs.biochem.7b01004

73. “Compound design guidelines for evading the efflux and permeation barriers of Escherichia coli with the oxazolidinone class of antibacterials: test case for a general approach to improving whole cell Gram-negative activity” Andrew Spaulding, Khuloud Takrouri, Poornachandran Mahalingam, Dillon Cleary, Harold Cooper, Paola Zucchi, Westley Tear, Bilyana Koleva, Penny J. Beuning, Elizabeth B. Hirsch, and James B. Aggen  Bioorganic & Medicinal Chemistry Letters 27 5310-5321 (2017). http://dx.doi.org/10.1016/j.bmcl.2017.10.01872

72.“Human Y-family DNA polymerase kappa is more tolerant to changes in its active site loop than its ortholog E. coli DinB” Nicole M. Antczak, Morgan Packer, Xueguang Lu, Ke Zhang, and Penny J. Beuning  Chemical Research in Toxicology 30 2002–2012. (2017) http://dx.doi.org/10.1021/acs.chemrestox.7b00175

71. “DNA Polymerases: From Molecular Mechanisms to Human Disease, a Special Issue” (editorial) Penny J. Beuning  Chemical Research in Toxicology 30 1921 (2017)

70. “A Professional Development Handbook for New Faculty” Dave Z. Besson, Penny J. Beuning, and Scott A. Snyder Educational and Outreach Projects from the Cottrell Scholars Collaborative, ACS Symposium Series (2017)

69. “Throwing away the cookbook: implementing course-based undergraduate research experiences (CUREs) in chemistry” Jennifer M. Heemstra, Rory Waterman, John M. Antos, Penny J. Beuning, Scott K. Bur, Linda Columbus, Andrew L. Feig, Amelia A. Fuller, Jason G. Gillmore, Aaron M. Leconte, Casey H. Londergan, William C. K. Pomerantz, Jennifer A. Prescher, and Levi M. StanleyEducational and Outreach Projects from the Cottrell Scholars Collaborative, ACS Symposium Series (2017)

68. “Identification of the dimer exchange interface of the bacterial DNA damage response protein UmuD” David A. Murison, Rebecca C. Timson, Bilyana N. Koleva, Michael Ordazzo, Penny J. Beuning Biochemistry 56 4773-4785 (2017)  http://dx.doi.org/10.1021/acs.biochem.7b00560

67. “Single-molecule mechanochemical characterization of E. coli pol III core catalytic activity” M. Nabuan Naufer, David A. Murison, Ioulia Rouzina, Penny J. Beuning, and Mark C. Williams Protein Science 26 1413–1426 (2017) http://dx.doi.org/10.1002/pro.3152

66. “NMR resonance assignments for the N-terminal domain of the δ subunit of the E. coli γ clamp loader complex” Esmael M. Alyami, Alessandro A. Rizzo, Penny J. Beuning, and Dmitry M. Korzhnev Biomolecular NMR Assignments 11 169-173 (2017) http://dx.doi.org/10.1007/s12104-017-9741-z

65. “Altering the N-terminal arms of the polymerase manager protein UmuD modulates protein interactions” David A. Murison, Jaylene N. Ollivierre, Qiuying Huang, David E. Budil, and Penny J. Beuning PLoS One 12e0173388 (2017) http://dx.doi.org/10.1371/journal.pone.0173388

64. “Research Skills and Ethics: The 20-year evolution of a professional development graduate course” Penny Beuning Analytical and Bioanalytical Chemistry 409 859-862 (2017) http://dx.doi.org/10.1007/s00216-016-9989-7

63. “Visualizing the non-homogeneous structure of RAD51 filaments using nanofluidic channels” Louise Fornander, Karolin Frykholm, Joachim Fritzsche, Joshua Araya, Philip Nevin, Erik Werner, Ali Cakir, Fredrik Persson, Edwige Garcin, Penny Beuning, Bernhard Mehlig, Mauro Modesti, Fredrik Westerlund Langmuir 32 8403-8412 (2016) http://dx.doi.org/10.1021/acs.langmuir.6b01877

62. “Progress against Escherichia coli with the oxazolidinone class of antibacterials: test case for a general approach to improving whole cell Gram-negative activity” Khuloud Takrouri, Harold Cooper, Andrew Spaulding, Paola Zucchi, Bilyana Koleva, Dillon Cleary, Westley Tear, Penny Beuning, Elizabeth Hirsch, and Jim Aggen ACS Infectious Diseases 2 405-426 (2016) http://dx.doi.org/10.1021/acsinfecdis.6b00003

Recommended article by F1000 Prime

61. “Local structure based method for prediction of the biochemical function of proteins: Applications to glycoside hydrolases” Ramya Parasuram, Caitlyn L. Mills, Zhouxi Wang, Saroja Somasundaram, Penny J. Beuning and Mary Jo Ondrechen Methods 93 51-63 (2016) http://dx.doi.org/10.1016/j.ymeth.2015.11.010

60. “Point mutations in Escherichia coli DNA pol V that confer resistance to non-cognate DNA damage also alter protein-protein interactions” Lisa A. Hawver, Mohammad Tehrani, Nicole M. Antczak, Danielle Kania, Stephanie Muser, Jana Sefcikova and Penny J. Beuning Mutation Research 780 1-14 (2015) http://dx.doi.org/10.1016/j.mrfmmm.2015.07.003

59. “Non-cognate DNA damage prevents formation of active conformation of Y-family DNA polymerases DinB and pol kappa” Philip Nevin, Xueguang Lu, Ke Zhang, John R. Engen, and Penny J. Beuning The FEBS Journal 282 2646–2660 (2015) http://dx.doi.org/10.1111/febs.13304

58. “Biochemical Functional Predictions for Protein Structures of Unknown or Uncertain Function” Caitlyn L. Mills, Penny J. Beuning, and Mary Jo Ondrechen Computational and Structural Biotechnology Journal 13 182-191 (2015) http://dx.doi.org/10.1016/j.csbj.2015.02.003

57. “Prediction of Distal Residue Participation in Enzyme Catalysis” Heather R. Brodkin, Nicholas A. DeLateur, Srinivas Somarowthu, Caitlyn L. Mills, Walter R. Novak, Penny J. Beuning, Dagmar Ringe, and Mary Jo Ondrechen Protein Science 24 762-778 (2015) http://dx.doi.org/10.1002/pro.2648

56. “Steric gate residues of Y-family DNA polymerases DinB and pol kappa are crucial for dNTP-induced conformational change” Philip Nevin, John R. Engen, and Penny J. Beuning DNA Repair 29 65-73 (2015) http://dx.doi.org/10.1016/j.dnarep.2015.01.012

55. “Structure activity relationship study of Mezzettiasides natural products and their four new disaccharide analogues for anticancer/antibacterial activity” Sumit O. Bajaj, Pei Shi, Penny J. Beuning and George A. O’Doherty MedChemComm 5 1138-1142 (2014) http://dx.doi.org/10.1039/C4MD00095A

54. “Cryptocaryol Structure-Activity Relationship Study of Cancer Cell Cytotoxicity and Ability to Stabilize PDCD4” Michael F. Cuccarese, Yanping Wang, Penny J. Beuning and George A. O’Doherty ACS Medicinal Chemistry Letters 5 522-526 (2014) http://dx.doi.org/10.1021/ml4005039

53. “Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics” Jing Fang, Philip Nevin, Visvaldas Kairys, Ceslovas Venclovas, John R. Engen and Penny J. Beuning Structure 22 572-581 (2014) http://dx.doi.org/10.1016/j.str.2014.02.001http://www.cell.com/structure/abstract/S0969-2126(14)00040-9

Preview: http://dx.doi.org/10.1016/j.str.2014.03.006

52. “Use of FRET to study dynamics of DNA replication” Philip Nevin and Penny J. Beuning in Chemical Biology of Nucleic Acids: Fundamentals and Clinical Applications V.A. Erdmann, W.T. Markiewicz, and J. Barciszewski, Eds., Springer, New York, NY 95-111 (2014) View book

51. “Polymerase manager protein UmuD directly regulates E. coli DNA polymerase III α binding to ssDNA” Kathy R. Chaurasiya, Clarissa Ruslie, Michelle C. Silva, Lukas Voortman, Philip Nevin, Samer Lone, Penny J. Beuning, and Mark C. Williams Nucleic Acids Research 41 8959-8968 (2013) http://dx.doi.org/10.1093/nar/gkt648

50. “Discrimination against major groove adducts by Y family polymerases of the DinB subfamily” Jason M. Walsh, Paul J. Ippoliti, Erin A. Ronayne, Eriks Rozners, and Penny J. Beuning DNA Repair 12 713-722 (2013) http://dx.doi.org/10.1016/j.dnarep.2013.05.006

49. “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, Vol. 4, 477-481 (2013). (encyclopedia chapter)

48. “Dimer exchange and cleavage specificity of the DNA damage response protein UmuD” Jaylene N. Ollivierre, Jacquelyn L. Sikora, and Penny J. Beuning Biochimica et Biophysica Acta-Proteins and Proteomics 1834 611–620 (2013) http://dx.doi.org/10.1016/j.bbapap.2012.11.008

47. “Structure Activity Relationship Study of the Cleistriosides and Cleistetrosides for Antibacterial/Anticancer Activity” Pei Shi, Michelle C. Silva, Hua-Yu Wang, Bulan Wu, Novruz Akhmedov, Miaosheng Li, Penny J. Beuning, George A. O’Doherty, ACS Medicinal Chemistry Letters 3 1086–1090 (2012) http://dx.doi.org/10.1021/ml300303g

46. “Multiple strategies for translesion synthesis in bacteria” Paul Ippoliti, Nicholas A. DeLateur, Kathryn M. Jones, Penny J. Beuning Cells 1 799-831 (2012) http://dx.doi.org/10.3390/cells1040799

45. “Effects of non-catalytic, distal amino acid residues on activity of E. coli DinB (DNA Polymerase IV)” Jason M. Walsh, Ramya Parasuram, Pradyumna R. Rajput, Eriks Rozners, Mary Jo Ondrechen and Penny J. Beuning Environmental and Molecular Mutagenesis 53 766-776 (2012) http://dx.doi.org/10.1002/em.21730

44. “Synthetic nucleotides as probes of DNA polymerase specificity” Jason M. Walsh and Penny J. Beuning, Journal of Nucleic Acids 2012 530963 (2012) http://dx.doi.org/10.1155/2012/530963

43. “Selective disruption of the DNA polymerase III α-β complex by the umuD gene products” Michelle C. Silva, Philip Nevin, Erin A. Ronayne, and Penny J. Beuning, Nucleic Acids Research 40 5511-5522 (2012) http://dx.doi.org/10.1093/nar/gks229

42. “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

41. “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

40. “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. BeuningMolecular BioSystems 7 3183-3186 (2011) dx.doi.org/10.1039/C1MB05334E

39. “Characterization of Escherichia coli UmuC Active Site Loops Identifies Variants that Confer UV Hypersensitivity” Lisa A. Hawver, Caitlin A. Gillooly, and Penny J. BeuningJournal of Bacteriology 193 5400-5411 (2011) dx.doi.org/10.1128/JB.05301-11

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 Bioinformatics79 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 Chemistry286 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). http://link.springer.com/content/pdf/10.1007%2F978-0-387-92808-1_11.pdf

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 B106 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 Chemistry276 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