Penny Beuning

Affiliated Faculty,  Bioengineering
Professor,  Chemistry and Chemical Biology



  • 617.373.2865

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Research Focus

chemical biology and biotechnology; DNA replication and repair; enzyme function


2000 Ph.D. University of Minnesota
1994 B.A. Macalester College, St. Paul, Minnesota

Honors & Awards

  • 2021, IMPACT Award, Research Corporation for Science Advancement
  • 2020, Fellow, American Chemical Society
  • 2012, American Cancer Society Research Scholar Award
  • 2009, National Science Foundation CAREER Award
  • 2009, Cottrell Scholar Award
  • Chemical Research in Toxicology Young Investigator Award, American Chemical Society

Research Overview

chemical biology and biotechnology; DNA replication and repair; enzyme function

Selected Research Projects

  • D3SC: Mining For Mechanistic Information to Predict Protein Function
    • – Co-Principal Investigator, National Science Foundation
  • Dynamics of Processivity Clamp Proteins in Bacterial DNA Replication
    • – Principal Investigator, National Institutes of Health

Selected Publications

  • Strezsak, Steven R., Beuning, Penny J., Skizim, Nicholas J. (2021) Complete Enzymatic Digestion of Double-Stranded RNA to Nucleosides Enables Accurate Quantification of dsRNA. Analytical Methods 13, 179-185. 10.1039/D0AY01498B
  • Naufer, M. Nabuan, Morse, Michael, Björg Möller, Guðfríður, McIsaac, James, Rouzina, Ioulia, Beuning, Penny J., Williams, Mark C. (2021) Multiprotein E. coli SSB-ssDNA complex show both stable binding and rapid dissociation due to interprotein interactions. Nucleic Acids Research 49, 1532-1549. 10.1039/nar/gkaa1267
  • L. Ngu, J.N. Winters, K. Nguyen, K.E. Ramos, N.A. DeLateur, L. Makowski, P.C. Whitford, M.J. Ondrechen, P.J. Beuning Probing Remote Residues Important for Catalysis in Escherichia Coli Ornithine Transcarbamoylase, PLoS One 15(2), 2020, e0228487
  • K.R. Moulton, A. Sadiki, B.N. Koleva, L.J. Ombelets, T.H. Tran, S. Liu, B. Wang, H. Chen, E. Micheloni, P.J. Beuning, G.A. O’Doherty, Z.S. Zhou, Site-Specific Reversible Protein Modification: Transglutaminase-Catalyzed Glutamine Conjugation and Bioorthogonal Light-Mediated Removal, Bioconjugate Chemistry, 30, 2019, 1617-1621
  • N.M. Antczak, A.R. Walker, H.R. Stern, E.M. Leddin, T.A. Coulther, C. Palad, R.J. Swett, G.A. Cisneros, P.J. Beuning, Characterization of Nine Cancer-Associated Variants in Human DNA Polymerase K, Chemical Research in Toxicology, 31, 2018, 697-711
  • C.L. Mills, R. Garg, J.S. Lee, L. Tian, A. Suciu, G. Cooperman, P.J. Beuning, M.J. Ondrechen, Functional Classification of Protein Structures by Local Structure Matching in Graph Representation, Protein Science, 27, 2018, 1125-1135
  • R. Parasuram, T.A. Coulther, J.M. Hollander, E. Keston Smith, M.J. Ondrechen, P.J. Beuning, Prediction of Active Site and Distal Residues in E. coli DNA Polymerase III Alpha Polymerase Activity, Biochemistry, 57(7), 2018, 1063–1072


Jun 27, 2019

Predicting Protein Functions from 3D Structures

ECE Professor Deniz Erdogmus (co-PI) and affiliated BioE Professors Mary Jo Ondrechen (PI) and Penny Beuning (co-PI) were awarded a $600K NSF grant for “Mining for mechanistic information to predict protein function”.


Aug 21, 2018

$1M NSF Grant to Advance the Study of Single-Molecule Research

BioE Professor Jeffrey Ruberti (co-PI) along with bioengineering affiliated and College of Science faculty, including Professor Mark Williams (PI), and Associate Professors Penny Beuning (co-PI), Meni Wanunu (co-PI), and Ke Zhang (co-PI) were awarded a $1M NSF grant for the “Acquisition of a Lumick’s SuperC-TRAP correlative optical tweezers and fluorescence microscope (CTFM) system.”

Mar 22, 2016

FY17 TIER 1 Award Recipients

23 COE faculty and affiliates were recipients of FY17 TIER 1 Interdisciplinary Research Seed Grants for 12 different projects representing over $600K dollars of investment in research.


Apr 06, 2011

FY12 TIER 1 Award Recipients

28 COE faculty and affiliates were recipients of FY12 TIER 1 Interdisciplinary Research Seed Grants for 18 different research projects.

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