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SUMMARY:Tangle analysis of protein-DNA complexes - Darcy\, I (University o
 f Iowa\, USA)
DTSTART:20120907T091000Z
DTEND:20120907T095000Z
UID:TALK39591@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Just like local knots can occur in long extension cords\, such
  knots can also appear in DNA. DNA can be be either linear or circular. So
 me proteins will cut DNA and change the DNA configuration before resealing
  the DNA. Thus\, if the DNA is circular\, the DNA can become knotted. Prot
 ein-DNA complexes were first mathematically modeled using tangles in Ernst
  and Sumners seminal paper\, "A calculus for rational tangles: application
 s to DNA recombination" (Math Proc Camb Phil Soc\, 1990). A tangle consist
 s of arcs properly embedded in a 3-dimensional ball. In order to model pro
 tein-bound DNA\, the protein is modeled by the 3D ball while the segments 
 of DNA bound by the protein can be thought of as arcs embedded within the 
 protein ball. This is a very simple model of protein-DNA binding\, but fro
 m this simple model\, much information can be gained. The main idea is tha
 t when modeling protein-DNA reactions\, one would like to know how to draw
  the DNA. For example\, are there any cr ossings trapped by the protein co
 mplex? How do the DNA strands exit the complex? Is there significant bendi
 ng? Tangle analysis cannot determine the exact geometry of the protein-bou
 nd DNA\, but it can determine the overall entanglement of this DNA\, after
  which other techniques may be used to more precisely determine the geomet
 ry.\n
LOCATION:Seminar Room 1\, Newton Institute
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