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Nucleic Acids Research Advance Access published online on January 30, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp043
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

DNA sampling: a method for probing protein binding at specific loci on bacterial chromosomes

Matej Butala1,2, Stephen J. W. Busby1,* and David J. Lee1

1School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK and 2Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, Ljubljana, Slovenia

*To whom correspondence should be addressed. Tel: +44 121 414 5439; Fax: +44 121 414 5425; Email: s.j.w.busby{at}bham.ac.uk

Received December 23, 2008. Revised January 14, 2009. Accepted January 14, 2009.

We describe a protocol, DNA sampling, for the rapid isolation of specific segments of DNA, together with bound proteins, from Escherichia coli K-12. The DNA to be sampled is generated as a discrete fragment within cells by the yeast I-SceI meganuclease, and is purified using FLAG-tagged LacI repressor and beads carrying anti-FLAG antibody. We illustrate the method by investigating the proteins bound to the colicin K gene regulatory region, either before or after induction of the colicin K gene promoter.


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