Coloring the Mu transpososome.
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.
Darcy
Isabel K
IK
Mathematics Department, University of Iowa, Iowa City, IA 52242, USA. idarcy@math.uiowa.edu
Chang
Jeff
J
Druivenga
Nathan
N
McKinney
Colin
C
Medikonduri
Ram K
RK
Mills
Stacy
S
Navarra-Madsen
Junalyn
J
Ponnusamy
Arun
A
Sweet
Jesse
J
Thompson
Travis
T
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
D004251:DNA Transposable Elements; D004278:DNA, Superhelical; D004279:DNA, Viral; D004268:DNA-Binding Proteins; C114697:mu transposase; C045073:Cre recombinase; D019426:Integrases; D019895:Transposases