Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites.
Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites.
Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
Julian
J
Kates-Harbeck
Antoine
A
Tilloy
Mara
M
Prentiss
D001665:Binding Sites; D004247:DNA / Q000378:metabolism; D004058:Diffusion; D008958:Models, Molecular; D011485:Protein Binding; D011938:Rec A Recombinases / Q000737:chemistry* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D013269:Stochastic Processes; D013816:Thermodynamics; D013997:Time Factors
D004247:DNA; D011938:Rec A Recombinases