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

  • 2012, American Cancer Society Research Scholar Award
  • 2009, National Science Foundation CAREER Award
  • 2009, Cottrell Scholar Award

Research Overview

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

Selected Publications

  • 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
  • N.M. Antczak, M. Packer, X. Lu, K. Zhang, P.J. Beuning, Human Y-family DNA Polymerase Kappa is more Tolerant to Changes in its Active Site Loop than its Ortholog E. coli DinB, Chemical Research in Toxicology, 30(11), 2017, 2002–2012
  • D.A. Murison, R.C. Timson, B.N. Koleva, M. Ordazzo, P.J. Beuning, Identification of the Dimer Exchange Interface of the Bacterial DNA Damage Response Protein UmuD, Biochemistry, 56, 2017, 4773-4785
  • D.A. Murison, J.N. Ollivierre, Q. Huang, D.E. Budil, P.J. Beuning, Altering the N-Terminal Arms of the Polymerase Manager Protein UmuD Modulates Protein Interactions, PLoS One, 12(3), 2017
  • M. Nabuan Naufer, D.A. Murison, I. Rouzina, P.J. Beuning, M.C. Williams, Single-Molecule Mechanochemical Characterization of E. coli pol III Core Catalytic Activity, Protein Science, 26(7), 2017, 1413-1426
  • P. Nevin, X. Lu, K. Zhang, J.R. Engen, P.J. Beuning, Non-Cognate DNA Damage Prevents Formation of Active Conformation of Y-family DNA Polymerases DinB and Pol Kappa, The FEBS Journal, 282, 2015, 2646-2660


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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