Model of RecA-mediated homologous recognition.
We consider theoretically the homology search between a long double-stranded DNA and a RecA-single-stranded DNA nucleofilament, emphasizing the polymeric nature of the search and the ability of double-stranded DNA to overcome the difference in pitch between itself and the nucleofilament by thermally activated stretching from the canonical B state to the metastable, stretched S state. Our analytical first-passage-time analysis agrees well with experimental data, predicts new dependencies on the intracellular fluid viscosity and ionic strength, and strongly suggests that initial homologous recognition involves a three base-pair seed.
Dorfman
Kevin D
KD
Laboratoire Physicochimie-Curie, CNRS/UMR 168, Institut Curie, 26 Rue d'Ulm, F-75248 Paris Cedex 5, France.
Fulconis
Renaud
R
Dutreix
Marie
M
Viovy
Jean-Louis
JL
D000251:Adenosine Triphosphatases; D001665:Binding Sites; D003198:Computer Simulation; D004265:DNA Helicases; D004269:DNA, Bacterial / Q000737:chemistry*; D004058:Diffusion; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D011485:Protein Binding; D011938:Rec A Recombinases / Q000737:chemistry*; D017385:Sequence Homology
D004269:DNA, Bacterial; D011938:Rec A Recombinases; D000251:Adenosine Triphosphatases; D004265:DNA Helicases