Skip to main content
SpringerLink
Log in
Book cover

The Bacterial Nucleoid pp 117–126Cite as

A Chromosome Co-Entrapment Assay to Study Topological Protein–DNA Interactions

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1624))

Abstract

Chromosome organization, DNA replication, and transcription are only some of the processes relying on dynamic and highly regulated protein–DNA interactions. Here, we describe a biochemical assay to study the molecular details of associations between ring-shaped protein complexes and chromosomes in the context of living cells. Any protein complex embracing chromosomal DNA can be enriched by this method, allowing for the underlying loading mechanisms to be investigated.

This is a preview of subscription content, log in via an institution.

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Bell SP, Kaguni JM (2013) Helicase loading at chromosomal origins of replication. Cold Spring Harb Perspect Biol 5:a010124

    PubMed  PubMed Central  Google Scholar 

  2. Costa A, Hood IV, Berger JM (2013) Mechanisms for initiating cellular DNA replication. Annu Rev Biochem 82:25–54

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Sherratt DJ, Arciszewska LK, Crozat E et al (2010) The Escherichia coli DNA translocase FtsK. Biochem Soc Trans 38:395–398

    Article  CAS  PubMed  Google Scholar 

  4. Lenhart JS, Pillon MC, Guarné A et al (2016) Mismatch repair in Gram-positive bacteria. Res Microbiol 167:4–12

    Article  CAS  PubMed  Google Scholar 

  5. Hauk G, Berger JM (2016) The role of ATP-dependent machines in regulating genome topology. Curr Opin Struct Biol 36:85–96

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Indiani C, O’Donnell M (2006) The replication clamp-loading machine at work in the three domains of life. Nat Rev Mol Cell Biol 7:751–761

    Article  CAS  PubMed  Google Scholar 

  7. Gligoris TG, Scheinost JC, Bürmann F et al (2014) Closing the cohesin ring: structure and function of its Smc3-kleisin interface. Science 346:963–967

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Samel SA, Fernández-Cid A, Sun J et al (2014) A unique DNA entry gate serves for regulated loading of the eukaryotic replicative helicase MCM2-7 onto DNA. Genes Dev 28:1653–1666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Wilhelm L, Bürmann F, Minnen A et al (2015) SMC condensin entraps chromosomal DNA by an ATP hydrolysis dependent loading mechanism in Bacillus subtilis. Elife 4:1–18

    Article  Google Scholar 

  10. Bürmann F, Shin H-C, Basquin J et al (2013) An asymmetric SMC-kleisin bridge in prokaryotic condensin. Nat Struct Mol Biol 20:371–379

    Article  PubMed  Google Scholar 

  11. Mawer JSP, Leach DRF (2013) Pulsed-field gel electrophoresis of bacterial chromosomes. In: Makovets S (ed) DNA electrophoresis: methods and protocols, vol 1054. Humana Press, Totowa, NJ, pp 187–194

    Chapter  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Research Group ‘Chromosome Organization and Dynamics’, Max Planck Institute of Biochemistry, Martinsried, Germany

    Larissa Wilhelm & Stephan Gruber

  2. Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Biophore, 1015, Lausanne, Switzerland

    Stephan Gruber

Authors
  1. Larissa Wilhelm
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stephan Gruber
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Stephan Gruber .

Editor information

Editors and Affiliations

  1. UMR CNRS 7241, INSERM U1050, CIRB, Collège de France, Paris, France

    Olivier Espéli

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Wilhelm, L., Gruber, S. (2017). A Chromosome Co-Entrapment Assay to Study Topological Protein–DNA Interactions. In: Espéli, O. (eds) The Bacterial Nucleoid. Methods in Molecular Biology, vol 1624. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7098-8_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7098-8_10

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7097-1

  • Online ISBN: 978-1-4939-7098-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation