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

Larissa Wilhelm; Stephan Gruber

doi:10.1007/978-1-4939-7098-8_10

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

Methods Mol Biol. 2017:1624:117-126. doi: 10.1007/978-1-4939-7098-8_10.

Authors

Larissa Wilhelm¹, Stephan Gruber^{2

3}

Affiliations

¹ Research Group 'Chromosome Organization and Dynamics', Max Planck Institute of Biochemistry, Martinsried, Germany.
² Research Group 'Chromosome Organization and Dynamics', Max Planck Institute of Biochemistry, Martinsried, Germany. Stephan.gruber@unil.ch.
³ Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Biophore, 1015, Lausanne, Switzerland. Stephan.gruber@unil.ch.

PMID: 28842880
DOI: 10.1007/978-1-4939-7098-8_10

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.

Keywords: Agarose plug; BMOE; Beta-clamp; Chromosome organization; Cysteine cross-linking; DNA entrapment; HaloTag labeling; Smc-ScpAB.

MeSH terms

Bacillus subtilis / genetics
Bacillus subtilis / metabolism
Bacterial Proteins / chemistry
Bacterial Proteins / metabolism
Binding Sites
Chromosomes, Bacterial / chemistry
Chromosomes, Bacterial / metabolism*
Cross-Linking Reagents
DNA-Binding Proteins / chemistry
DNA-Binding Proteins / metabolism*
Protein Binding

Substances

Bacterial Proteins
Cross-Linking Reagents
DNA-Binding Proteins