Share this page: More

James M. Berger

James C. Barrow
Department Affiliation: Primary: Biophysics and Biophysical Chemistry; Secondary: Pharmacology and Molecular Sciences; Oncology
Degree: Ph.D., Harvard University
Rank: Professor
Telephone Number: 410-955-7163
Fax Number: 410-955-0637
E-mail address:
School of Medicine Address: Wood Basic Science 713,
725 N. Wolfe Street, Baltimore, MD  21205

Structural and catalytic mechanisms of nucleic-acid machines and assemblies; control of DNA replication and chromosome superstructure; small-molecule and biological regulatory mechanisms.

Research in my laboratory is focused on understanding the molecular mechanisms and cellular functions of multisubunit assemblies that control the organization, preservation, and flow of genetic information. We are particularly interested in developing real-time, atomic-level models that explain how chemical energy is transduced into force and motion, and how dynamic assemblies control DNA replication, gene expression, chromosome superstructure, and other essential nucleic-acid transactions.

My group’s approach relies on a blend of structural, biochemical, and biophysical methods to define the architecture, function, evolution, and regulation of biological complexes. X-ray crystallography and traditional biochemistry have traditionally formed the core of our approach; however, we are increasingly merging these methods with other experimental tools such as small-angle X-ray scattering, single-molecule studies, and electron microscopy. Since the inception of the group in 1995, we have biochemically and structurally defined the range and nature of key functional intermediates and transitions for a variety of nucleotide-dependent ‘molecular machines,’ including topoisomerases, helicases, condensins, and replication initiation complexes.

I have had a strong interest in training throughout my career. While at Berkeley, I served as Head Graduate Advisor for the Department of Molecular and Cell Biology and I oversaw the construction and implementation of a new graduate course curriculum. At Johns Hopkins, I have served as the Director of our department’s first-year medical student course. To date, I have mentored a total of 28 doctoral students and 26 post-doctoral fellows. Of those who have moved on from the lab, nearly all (>95%) have gone on to productive careers in academia (20), biotechnology/pharma (14), law (4), and medicine (1). The remainder are gainfully employed in activities such as teaching and consulting.

A complete list of our publications, excluding chapters and articles not accessed by PubMed, can be found at:


Representative Publications:  

  • Parker, M.W., Bell, M., Mir, M., Kao, J.A., Darzacq, X., Botchan, M.R.*, Berger, J.M.* (*co-corresponding authors). A new class of disordered elements controls DNA replication through initiator self-assembly. Elife 2019 Sep 27;8, 2019. pii: e48562. (Accompanying InsightElife, 2019). Pub Med Reference
  • Blower, T.R., Bandak, A., Lee, A.S.Y., Austin, C.A., Nitiss, J.L., Berger, J.M. A complex suite of loci and elements in eukaryotic type II topoisomerases determine selective sensitivity to distinct poisoning agents. Nucleic Acids Res. 2019 Sep 5;47(15):8163-8179. Pub Med Reference
  • Arias-Palomo, E.*, Puri, N., O'Shea Murray, V.L., Yan, Q., Berger, J.M.* (*co-corresponding authors). Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA. Mol Cell. 2019 Apr 4;74(1):173-184. Pub Med Reference
  • Lawson, M.R., Ma, W., Bellecourt, M.J., Artsimovitch, I., Martin, A., Landick, R., Schulten, K., Berger, J.M. Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein. Mol Cell. 2018 Sep 20;71(6):911-922. Pub Med Reference
  • Bleichert, F., Leitner, A., Aebersold, R., Botchan, M.R.*, Berger, J.M.* (*co-corresponding authors). Conformational control and DNA-binding mechanism of the metazoan origin recognition complex. Proc Natl Acad Sci U S A. 2018;115(26): E5906-E5915. Pub Med Reference
  • Wendorff, T.J. and Berger, J.M. Topoisomerase VI senses and exploits both DNA crossings and bends to facilitate strand passage. Elife 2018, Mar 29;7. Pub Med Reference
  • Lee, J.H., Wendorff, T.J., Berger, J.M. Resveratrol: a novel type of topoisomerase II inhibitor. J Biol Chem. 2017 Dec 22;292(51):21011-21022.  Pub Med Reference
  • Thomsen, N.D., Lawson, M.R., Witkowsky, L.B., Qu, S., Berger, J.M. Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor. Proc Natl Acad Sci U S A 2016 Nov 29;113(48): E7691-E7700. Pub Med Reference
  • Hood, I.V., Berger, J.MElife. Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication. Elife 2016 May 31;5. Pub Med Reference


Other graduate programs in which Dr. Berger participates: