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Book: Penny J. Beuning, Dave Z. Besson, Scott A. Snyder, and Nicola L. B. Pohl with an annotated bibliography by Ingrid DeVries Salgado and Amy Blondin Hotchkiss, ISBN 978-0-692-26580-2 “Teach Better, Save Time, and Have More Fun: A Guide to Teaching and Mentoring in Science” (2022) Second Ed.

Interactive on-line version:

First Ed. 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.

101. “Biochemical activity of seventeen cancer associated variants of DNA polymerase kappa predicted by electrostatic properties” Lakindu S. Pathira Kankanamge, Alexandra Mora, Mary Jo Ondrechen and Penny J. Beuning Chemical Research in Toxicology 36 1789-1803. (2023) DOI: 10.1021/acs.chemrestox.3c00233 

100. “Functional annotation of haloacid dehalogenase superfamily structural genomics proteins” Lakindu S. Pathira Kankanamge, Lydia A. Ruffner, Mong Mary Touch, Manuel Pina, Penny J. Beuning, Mary Jo Ondrechen Biochemical Journal 480 1553-1569. (2023) DOI: 10.1042/BCJ20230057

99. “DNA damage alters binding conformations of E. coli single-stranded DNA binding protein” Michael Morse, Francesco Navarro Roby, Mansi Kinare, James McIsaac, Mark C. Williams, Penny J. Beuning Biophysical Journal 122 3950-3958. (2023) DOI: 10.1016/j.bpj.2023.08.018

98. “Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates” Michael Morse, Jana Sefcikova, Ioulia Rouzina, Penny J. Beuning, Mark C. Williams Nucleic Acids Research 51 290-303. (2023) DOI: 10.1093/nar/gkac1179

97. “A novel mobile phase to control charge states and metal adducts in the LC/MS for mRNA characterization assays” Steven R. Strezsak, Alyssa Pimentel, Ian Hill, Penny J. Beuning, Nicholas J. Skizim ACS Omega 7 22181-22191. (2022) DOI: 10.1021/acsomega.2c00185

96. “ILV Methyl NMR Resonance Assignments of the 81 kDa E. coli β-clamp” Socheata Lim, Sam Mahdi, Penny J. Beuning, and Dmitry M. Korzhnev NMR Assignments 16 317-323. (2022) DOI: 10.1007/s12104-022-10097-0

95. “Stereoselective synthesis of β-Glycinamide Ribonucleotide” Lisa Ngu, Debarpita Ray, Samantha S. Watson, Penny J. Beuning, Mary Jo Ondrechen, and George A O’Doherty Molecules 27 2528. (2022) DOI: 10.3390/molecules27082528.

94. “Functional Characterization of Structural Genomics Proteins in the Crotonase Superfamily” Caitlyn L. Mills, Pengcheng Yin, Becky Leifer, Lori Ferrins, George A. O’Doherty, Penny J. Beuning, Mary Jo Ondrechen ACS Chemical Biology 17 395-403. (2022) DOI: 10.1021/acschembio.1c00842.

93. “Versatile separation of nucleotides from bacterial cell lysates using strong anion exchange chromatography” Steven R. Strezsak, Penny J. Beuning, and Nicholas J. Skizim Journal of Chromatography B 1188 123044. (2021) DOI: 10.1016/j.jchromb.2021.123044

92. “Division of Chemical Toxicology Program at the American Chemical Society National Meeting: Celebrating 25 Years! ” Penny J. Beuning and Michael A. Trakselis Chemical Research in Toxicology 34 2167-2168 (2021) (editorial)

91. “Adapting undergraduate research to remote work to increase engagement” Susan E. Cohen, Sara M. Hashmi, A-Andrew D. Jones, III, Vasiliki Lykourinou, Mary Jo Ondrechen, Srinivas Sridhar, Anne L. van de Ven, Lauren S. Waters, and Penny J. Beuning The Biophysicist 2 28–32 (2021)

90. “NMR resonance assignments for the nucleotide binding domains of the E. coli clamp loader complex γ subunit” Sam Mahdi, Irina Bezsonova, Penny J. Beuning and Dmitry Korzhnev Biomolecular NMR Assignments 15 281-285 (2021)

89. “DNA Polymerase III, Bacterial” Melissa L. Liriano, Ryan J. Dilworth, and Penny J. Beuning, Ryan J. Dilworth and Hannah R. Stern Encyclopedia of Biological Chemistry 3rd edition Joe Jez, Ed., Elsevier Science, vol 4, 334-344. (2021)

88. ” UmuC D Lesion Bypass DNA Polymerase V ” Penny J. Beuning, Ryan J. Dilworth and Hannah R. Stern Encyclopedia of Biological Chemistry 3rd edition Joe Jez, Ed., Elsevier Science, vol 4, 334-344. (2021)

87. DNA Adductomics by Mass Tag Prelabeling” Poguang Wang, Elisabeth Roider, Michael E. Coulter, Christopher A. Walsh, Caitlin S. Kramer, Penny J. Beuning and Roger W. Giese Rapid Communications in Mass Spectrometry 35 e9095 (2021)

86. “Multiprotein E. coli SSB-ssDNA complex show both stable binding and rapid dissociation due to interprotein interactions” M. Nabuan Naufer, Michael Morse, Guðfríður Björg Möller, James McIsaac, Ioulia Rouzina, Penny J. Beuning and Mark C. Williams Nucleic Acids Research 49 1532-1549 (2021)

85. “Complete Enzymatic Digestion of Double-Stranded RNA to Nucleosides Enables Accurate Quantification of dsRNA” Steven Robert Strezsak, Penny J. Beuning and Nicholas Skizim Analytical Methods 13 179-185 (2021) DOI: 10.1039/D0AY01498B

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 31 1641–1646 (2020)

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)

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

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)

80. “Engineering polymerases for new functions” Timothy A. Coulther, Hannah R. Stern, and Penny J. Beuning Trends in Biotechnology (2019)

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)

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)

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)

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)

75. “A practical synthesis of glycinamide ribonucleotide” Debarpita Ray, Penny J. Beuning, Mary Jo Ondrechen, and George O’Doherty Heterocycles 97 (2018)

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)

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).

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)

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)

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)

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)

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)

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)

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)

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)

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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)

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)

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)

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)

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)

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)

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)

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)

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)


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)

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)

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)

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)

46. “Multiple strategies for translesion synthesis in bacteria” Paul Ippoliti, Nicholas A. DeLateur, Kathryn M. Jones, Penny J. Beuning Cells 1 799-831 (2012)

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)

44. “Synthetic nucleotides as probes of DNA polymerase specificity” Jason M. Walsh and Penny J. Beuning, Journal of Nucleic Acids 2012 530963 (2012)

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)

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)

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)

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)

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)

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)

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)

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)

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)

34. “Escherichia coli Y Family DNA Polymerases” Jason M. Walsh, Lisa A. Hawver, and Penny J. Beuning Frontiers in Bioscience 16 3164-3182 (2011)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)<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)

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)

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)

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)