The faithful propagation of genetic material is essential to life. A central prerequisite to the copying of DNA is the dedicated assembly of replicative machineries at proper sites on the chromosome. This replication "initiation" event depends on multiple components, including: 1) initiators, ATPases that bind origins and recruit other proteins to the replication start site, 2) helicase-loaders, which deposit replicative helicases onto DNA, and 3) primases, enzymes that create short oligonucleotides for extension by DNA polymerases. A long-term objective of our research has been to understand the molecular structure/function relationships that govern the initiation of DNA replication. Many of the proteins responsible for initiation have been identified, and a preliminary framework for their action is in place. However, there remains a host of outstanding questions regarding how these factors act individually and cooperatively to construct a competent replication fork. Our prior efforts in this area have generated new mechanistic models for initiator action, helicase loading, and priming that we are now in an ideal position to test. Using a combination of structural, biochemical, and biophysical methods we aim to: 1) Define how ATP controls DNA binding and remodeling by prokaryotic initiators, 2) Determine how ATP regulates bacterial helicase-loader assembly and function, and 3) Establish how the bacterial primase synthesizes primers and is inhibited by disparate types of small-molecule agents, including the stringent response regulator, (p)ppGpp. Together, these efforts will impact a number of scientific fronts, from understanding how origins are engaged and restructured to promote replisome construction, to defining how chemical energy and small-molecule inhibitors control the function of dynamic macromolecular machines. Knowledge of these processes is necessary for understanding how cells ultimately avoid initiation errors linked to genomic instabilities, transformation, and neoplasia.

Public Health Relevance

The faithful propagation of genetic material is essential to life. The goal of our research is understand the structure/function relationships that govern the initiation of DNA replication at a molecular level. Knowledge of these events is necessary for understanding how cells ultimately avoid errors linked to genomic instabilities and cancer onset.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-GGG-H (02))
Program Officer
Preusch, Peter C
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Berkeley
Schools of Arts and Sciences
United States
Zip Code
Costa, Alessandro; Renault, Ludovic; Swuec, Paolo et al. (2014) DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome. Elife 3:e03273
O'Shea, Valerie L; Berger, James M (2014) Loading strategies of ring-shaped nucleic acid translocases and helicases. Curr Opin Struct Biol 25:16-24
Strycharska, Melania S; Arias-Palomo, Ernesto; Lyubimov, Artem Y et al. (2013) Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Mol Cell 52:844-54
Duderstadt, Karl E; Berger, James M (2013) A structural framework for replication origin opening by AAA+ initiation factors. Curr Opin Struct Biol 23:144-53
Arias-Palomo, Ernesto; O'Shea, Valerie L; Hood, Iris V et al. (2013) The bacterial DnaC helicase loader is a DnaB ring breaker. Cell 153:438-48
Costa, Alessandro; Hood, Iris V; Berger, James M (2013) Mechanisms for initiating cellular DNA replication. Annu Rev Biochem 82:25-54
Costa, Alessandro; Ilves, Ivar; Tamberg, Nele et al. (2011) The structural basis for MCM2-7 helicase activation by GINS and Cdc45. Nat Struct Mol Biol 18:471-7
Duderstadt, Karl E; Chuang, Kevin; Berger, James M (2011) DNA stretching by bacterial initiators promotes replication origin opening. Nature 478:209-13
Lyubimov, Artem Y; Strycharska, Melania; Berger, James M (2011) The nuts and bolts of ring-translocase structure and mechanism. Curr Opin Struct Biol 21:240-8
Duderstadt, Karl E; Mott, Melissa L; Crisona, Nancy J et al. (2010) Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator. J Biol Chem 285:28229-39

Showing the most recent 10 out of 26 publications