title: Coloring the Mu transpososome.
abstract: BACKGROUND
  Tangle analysis has been applied successfully to study proteins which bind two segments of DNA and can knot and link circular DNA. We show how tangle analysis can be extended to model any stable protein-DNA complex.
  
  
  RESULTS
  We discuss a computational method for finding the topological conformation of DNA bound within a protein complex. We use an elementary invariant from knot theory called colorability to encode and search for possible DNA conformations. We apply this method to analyze the experimental results of Pathania, Jayaram, and Harshey (Cell 2002). We show that the only topological DNA conformation bound by Mu transposase which is biologically likely is the five crossing solution found by Pathania et al (although other possibilities are discussed).
  
  
  CONCLUSIONS
  Our algorithm can be used to analyze the results of the experimental technique described in Pathania et al in order to determine the topological conformation of DNA bound within a stable protein-DNA complex.
authors.affiliation: Mathematics Department, University of Iowa, Iowa City, IA 52242, USA. idarcy@math.uiowa.edu
authors.forename: Isabel K
authors.initials: IK
authors.lastname: Darcy
authors.forename: Jeff
authors.initials: J
authors.lastname: Chang
authors.forename: Nathan
authors.initials: N
authors.lastname: Druivenga
authors.forename: Colin
authors.initials: C
authors.lastname: McKinney
authors.forename: Ram K
authors.initials: RK
authors.lastname: Medikonduri
authors.forename: Stacy
authors.initials: S
authors.lastname: Mills
authors.forename: Junalyn
authors.initials: J
authors.lastname: Navarra-Madsen
authors.forename: Arun
authors.initials: A
authors.lastname: Ponnusamy
authors.forename: Jesse
authors.initials: J
authors.lastname: Sweet
authors.forename: Travis
authors.initials: T
authors.lastname: Thompson
mesh_terms: D000465:Algorithms; D010583:Bacteriophage mu / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D004251:DNA Transposable Elements / Q000235:genetics*; D004278:DNA, Superhelical / Q000737:chemistry* / Q000235:genetics; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D019426:Integrases / Q000737:chemistry / Q000378:metabolism; D008956:Models, Chemical; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012984:Software; D019895:Transposases / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D004278:DNA, Superhelical; D004279:DNA, Viral; D004268:DNA-Binding Proteins; C114697:mu transposase; C045073:Cre recombinase; D019426:Integrases; D019895:Transposases