Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 88, Issue 1, 2013, Pages

  Kates Harbeck, Julian ^a   Tilloy, Antoine ^a   Prentiss, Mara ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIASED RANDOM WALK; LONG-LINEAR ARRAY; WEAKLY NON-LINEAR;

CONFORMATIONS; SELF ASSEMBLY;

PROTEINS;

DNA; PROTEIN BINDING; RECA PROTEIN;

BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DIFFUSION; METABOLISM; SEQUENCE HOMOLOGY; STATISTICS; THERMODYNAMICS; TIME;

BINDING SITES; DIFFUSION; DNA; MODELS, MOLECULAR; PROTEIN BINDING; REC A RECOMBINASES; SEQUENCE HOMOLOGY, AMINO ACID; STOCHASTIC PROCESSES; THERMODYNAMICS; TIME FACTORS;

EID: 84880222144     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.88.012702     Document Type: Article

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36. In contrast, in a system with a binding energy proportional to the number of bound triplets, adding more triplets would always be either favorable or unfavorable regardless of the number bound; therefore, either initial testing will be unfavorable, or the sequence independent binding would become increasingly deeply bound as more triplets were added, resulting in kinetic trapping.
37. In vitro experiments featuring a single mismatched triplet followed by a series of matched triplets do show that skipping over a single triplet is not forbidden if subsequent regions contain substantial accidental homology.