James M. Berger, Ph.D.

Headshot of James M. Berger
  • Director, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine
  • Professor of Biophysics and Biophysical Chemistry

Research Interests

Small-molecule and biological regulatory mechanisms; Control of DNA replication and chromosome superstructure; Structural and catalytic mechanisms of nucleic-acid machines and assemblies ...read more


Dr. James Berger holds the Michael and Ann Hankin and Partners of Brown Advisory Professorship in Scientific Innovation. He is the director of the Institute for Basic Biomedical Sciences, professor of biophysics and biophysical chemistry at the Johns Hopkins University School of Medicine and co-director of the Cancer Chemical and Structural Biology Program for the Johns Hopkins Kimmel Cancer Center. His research focuses on how multi-subunit assemblies use adenosine triphosphate (ATP) for transferring energy within the chromosome and controlling the flow of genetic information. Dr. Berger has a twenty year history of studying the fundamental mechanisms of enzymes that control cell proliferation and small molecule inhibitors that target such systems.

Dr. Berger received his undergraduate degree in biochemistry from the University of Utah. He earned his Ph.D. from Harvard University and completed a fellowship at the Whitehead Institute at MIT.

Dr. Berger works with a number of graduate programs at Johns Hopkins and oversees a busy lab. He was elected to the National Academy of Sciences in 2013.

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  • Director, Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine
  • Michael and Ann Hankin and Partners of Brown Advisory Professor in Scientific Innovation
  • Co-Director, Cancer Chemical and Structural Biology Program, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center
  • Professor of Biophysics and Biophysical Chemistry
  • Professor of Oncology
  • Professor of Pharmacology and Molecular Sciences

Departments / Divisions

Centers & Institutes



  • Ph.D.; Harvard University (Massachusetts) (1995)
  • B.S.; University of Utah (Utah) (1990)

Research & Publications

Research Summary

Dr. Berger and his team’s current research examines replication initiation and replisome assembly. To better understand how cells regulate and initiate replication of their genomes, Berger and his colleagues are studying origin-binding proteins, helicases, primases and accessory remodeling factors from a variety of organisms within the three cellular domains of life. Work from their group is revealing important information about the mechanisms of origin processing, primer synthesis, and macromolecular assembly that occur during replisome construction. Dr. Berger’s team is also studying the nucleic acid-dependent motors, with a particular focus on a variety of DNA- and RNA-dependent motor proteins. They are working to determine how such proteins interact with nucleic acids and partner proteins, and how they use ATP to drive the architectural changes required for catalysis and physical movement.

One area of research focus is the study of DNA topoisomerases, which are well-established, clinically-validated targets of several anti-cancer agents. Dr. Berger's team has solved structures of topoisomerase targets in complex with target DNA substrates and various drugs. The goal is to understand mechanisms of drug resistance and cross-reactivity and to guide the discovery and development of new compounds with improved therapeutic potential. Dr. Berger's laboratory is also exploring whether the protein machinery responsible for initiating DNA replication can be exploited as a novel anti-cancer target. Additional research in Dr. Berger's laboratory is focused on understanding the molecular mechanisms and cellular functions of multisubunit assemblies that control the organization, preservation, and flow of genetic information. They are developing 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. The approach relies on a blend of structural, biochemical, and biophysical methods to define the architecture, function, evolution, and regulation of protein/nucleic acid complexes. X-ray crystallography and biochemistry have traditionally formed the core of his team's approach; however, they are increasingly merging these methods with other experimental tools such as small-angle X-ray scattering, single-molecule approaches, and electron microscopy. His lab has biochemically and structurally defined the range and nature of key functional intermediates and structural transitions for a variety of nucleotide-dependent “molecular machines,” including topoisomerases, helicases, condensins, and replication initiation complexes. These efforts have defined how biological systems use these factors to organize, transport, and reshape target nucleic-acid substrates at a physical level, and how their actions are controlled by both protein-protein interactions and small-molecule agents.


Lab Website: Berger Lab

Selected Publications

View all on PubMed

Mustaev A, Malik M, Zhao X, Kurepina N, Luan G, Oppegard LM, Hiasa H, Marks KR, Kerns RJ, Berger JM, Drlica K. “Fluoroquinolone-Gyrase-DNA Complexes: Two Modes of Drug Binding.” J Biol Chem. 2014 Feb 4.

Toske SG, Morello DR, Berger JM, Vazquez ER. “The use of δ13C isotope ratio mass spectrometry for methamphetamine profiling: comparison of ephedrine and pseudoephedrine-based samples to P2P-based samples.” Forensic Sci Int. 2014 Jan;234:1-6. doi: 10.1016/j.forsciint.2013.10.022. Epub 2013 Oct 31.

Strycharska MS, Arias-Palomo E, Lyubimov AY, Erzberger JP, O'Shea VL, Bustamante CJ, Berger JM. “Nucleotide and partner-protein control of bacterial replicative helicase structure and function.” Mol Cell. 2013 Dec 26;52(6):844-54. doi: 10.1016/j.molcel.2013.11.016.

Bleichert F, Balasov M, Chesnokov I, Nogales E, Botchan MR, Berger JM. “A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation.” Elife. 2013 Oct 8;2:e00882. doi: 10.7554/eLife.00882.

Vos SM, Stewart NK, Oakley MG, Berger JM. “Structural basis for the MukB-topoisomerase IV interaction and its functional implications in vivo.” EMBO J. 2013 Nov 13;32(22):2950-62. doi: 10.1038/emboj.2013.218. Epub 2013 Oct 4.

Academic Affiliations & Courses

Graduate Program Affiliation

Pharmacology and Molecular Sciences

Program in Molecular Biophysics (PMB)

Biochemistry, Cellular and Molecular Biology Graduate Program (BCMB)

Chemistry-Biology Interface Graduate Program

Activities & Honors


  • National Academy of Sciences, 2013
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