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Nucleic Acids Research Advance Access published online on November 26, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm1030
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© 2007 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.

Molecular Biology

DNA tape measurements of AraC

Michael E. Rodgers and Robert Schleif*

Biology Department, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA

*To whom correspondence should be addressed. Tel: +1 410 516 5206; Fax: +1 410 516 5213; Email: schleif{at}jhu.edu

Received August 24, 2007. Revised October 16, 2007. Accepted October 29, 2007.

A new method for measuring distances between points in the AraC–DNA complex was developed and applied. It utilizes variable lengths of single-stranded DNA that connect double-stranded regions containing the two half-site binding sequences of AraC. These distances plus the protein interdomain linker distances are compatible with two classes of structure for the dimeric AraC gene regulatory protein. In one class, the N-terminal regulatory arm of one dimerization domain is capable of interacting with the DNA-binding domain on the same polypeptide chain for a cis interaction. In the other class, the possible arm-DNA-binding domain interaction is trans, where it adds to the dimerization interface.


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