The Berger Group
Welcome to the laboratory of James M. Berger, located in the Department of Biophysics and Biophysical Chemistry. My laboratory’s research is focused on understanding how multi-subunit assemblies use ATP for overcoming topological challenges within the chromosome and controlling the flow of genetic information. We are particularly interested in developing mechanistic models that explain how macromolecular machines transduce chemical energy into force and motion, and in determining how cells exploit these complexes and their activities for regulating the initiation of DNA replication, chromosome superstructure, and other essential nucleic acid transactions. Our principal approaches rely on a variety of structural, biochemical, and biophysical methods to define the architecture, function, evolution, and regulation of biological complexes. We also have extensive interests in mechanistic enzymology and the study of small-molecule inhibitors of therapeutic potential, the development of chemical approaches to trapping weak protein/protein and protein/nucleic acid interactions, and in using microfluidics for biochemical investigations of protein dynamics and structure.
Selected Recent Publications
Liu C, Hauk G, Yan Q, Berger JM. Structure of Escherichia coli exonuclease VII. Proc Natl Acad Sci U S A. 2024 Jan 30;121(5):e2319644121.
Bandak AF, Blower TR, Nitiss KC, Gupta R, Lau AY, Guha R, Nitiss JL, Berger JM. Naturally mutagenic sequence diversity in a human type II topoisomerase. Proc Natl Acad Sci U S A. 2023 Jul 11;120(28):e2302064120
Jeong J, Lee JH, Carcamo CC, Parker MW, Berger JM. DNA-Stimulated Liquid-Liquid phase separation by eukaryotic topoisomerase II modulates catalytic function. Elife. 2022 Nov 7;11:e81786
Lee JH, Mosher EP, Lee YS, Bumpus NN, Berger JM. Control of topoisomerase II activity and chemotherapeutic inhibition by TCA cycle metabolites. Cell Chem Biol. 2021 Sep 11:S2451-9456(21)00403-7.
Puri N, Fernandez AJ, O’Shea Murray VL, McMillan S, Keck JL, Berger JM. The molecular coupling between substrate recognition and ATP turnover in a AAA+ hexameric helicase loader. Elife. 2021 May 26;10:e64232
Attali I, Botchan MR, Berger JM. Structural Mechanisms for Replicating DNA in Eukaryotes. Annu Rev Biochem. 2021 Jun 20;90:77-106.
Modulated control of DNA supercoiling balance by the DNA-wrapping domain of bacterial gyrase.
Hobson MJ, Bryant Z, Berger JM. Nucleic Acids Res. 2020 Feb 28;48(4):2035-2049.
Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA.
Arias-Palomo E, Puri N, O’Shea Murray VL, Yan Q, Berger JM. Mol Cell. 2019 Apr 4;74(1):173-184.
A new class of disordered elements controls DNA replication through initiator self-assembly.
Parker MW, Bell M, Mir M, Kao JA, Darzacq X, Botchan MR, Berger JM. Elife. 2019 Sep 27;8. pii: e48562.