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SUMMARY:Simulated looping propensities of protein-decorated DNA - Olson\, 
 W (Rutgers University\, New Jersey\, USA)
DTSTART:20120905T160000Z
DTEND:20120905T164000Z
UID:TALK39541@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Although the genetic messages in DNA are stored in a linear se
 quence of base pairs\, the genomes of living species do not function in a 
 linear fashion. Gene expression is regulated by DNA elements that often li
 e far apart along the genomic sequence but come close together during gene
 tic processing. The intervening residues form loops\, which are organized 
 by the binding of various proteins. For example\, in E. coli the Lac repre
 ssor protein assembly binds two DNA operators\, separated by 92 or 401 bas
 e pairs\, and suppresses the formation of gene products involved in the me
 tabolism of lactose. The system also includes several highly abundant arch
 itectural proteins\, such as Fis and HU\, which\, upon binding\, bend a do
 uble-helical turn of DNA by 45 degrees or more. In order to gain a better 
 understanding of the mechanics of DNA looping\, we have investigated the e
 ffects of various proteins on the configurational properties of fragments 
 of DNA\, treating the DNA with elastic potentials t hat consider the intri
 nsic structure and deformability of successive base pairs and incorporatin
 g the known three-dimensional structural effects of various proteins on DN
 A double-helical structure. The presentation will highlight some of the ne
 w models and computational techniques that we have developed to generate t
 he three-dimensional configurations of protein-mediated DNA loops and illu
 strate new insights gained from this work about the effects of various pro
 teins on DNA topology and the apparent contributions of non-specific bindi
 ng proteins to gene expression.\n
LOCATION:Seminar Room 1\, Newton Institute
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