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Nucleic Acids Research Advance Access originally published online on June 23, 2008
Nucleic Acids Research 2008 36(12):4204-4210; doi:10.1093/nar/gkn389
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Nucleic Acids Research, 2008, Vol. 36, No. 12 4204-4210
© 2008 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.

Structural Biology

The antiparallel loops in gal DNA

Giuseppe Lia1, Szabolcs Semsey2, Dale E. A. Lewis3, Sankar Adhya3, David Bensimon4, David Dunlap5 and Laura Finzi6,*

1Department of Chemistry, Harvard University, Cambridge, MA, USA, 2Department of Genetics, Eötvös Lóránd University, H-1117 Budapest, Hungary, 3Laboratory of Molecular Biology, NIH, Bethesda, MD, USA, 4Laboratoire de Physique Statistique, Ecole Normal Superieure, Paris, France, 5Department of Cell Biology and 6Department of Physics, Emory University, Atlanta, GA, USA

*To whom correspondence should be addressed. Tel: +1 404 727 4930; Fax: +1 404 727 0873; Email: lfinzi{at}emory.edu

Received March 8, 2008. Revised June 2, 2008. Accepted June 4, 2008.

Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein–DNA and protein–protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamically and biologically distinct. For example, theoretical models of Gal repressor/HU-mediated DNA-looping suggest that the antiparallel DNA loops, A1 and A2, are thermodynamically quite different. They are also biologically different, since in experiments using DNA molecules engineered to form only one of the two loops, the A2 loop failed to repress in vitro transcription. Surprisingly, single molecule measurements show that both loop trajectories form and that they appear to be quite similar energetically and kinetically.


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