antiparallel loops in gal DNA

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...

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Bibliographic Details
Published in:Nucleic acids research 2008-07, Vol.36 (12), p.4204-4210
Main Authors: Lia, Giuseppe, Semsey, Szabolcs, Lewis, Dale E.A, Adhya, Sankar, Bensimon, David, Dunlap, David, Finzi, Laura
Format: Article
Language:English
Subjects:
Bacterial Proteins - metabolism
DNA, Bacterial - chemistry
DNA, Bacterial - metabolism
DNA-Binding Proteins - metabolism
Escherichia coli Proteins - metabolism
Kinetics
Models, Molecular
Nucleic Acid Conformation
Operator Regions, Genetic
Repressor Proteins - metabolism
Structural Biology
Thermodynamics
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkn389