title: RecA-mediated sequence homology recognition as an example of how searching speed in self-assembly systems can be optimized by balancing entropic and enthalpic barriers.
abstract: Ideally, self-assembly should rapidly and efficiently produce stable correctly assembled structures. We study the tradeoff between enthalpic and entropic cost in self-assembling systems using RecA-mediated homology search as an example. Earlier work suggested that RecA searches could produce stable final structures with high stringency using a slow testing process that follows an initial rapid search of ∼9-15 bases. In this work, we will show that as a result of entropic and enthalpic barriers, simultaneously testing all ∼9-15 bases as separate individual units results in a longer overall searching time than testing them in groups and stages.
authors.affiliation: Harvard University, Department of Physics, Cambridge, Massachusetts 02138, USA.
authors.forename: Lili
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Harvard University, Department of Physics, Cambridge, Massachusetts 02138, USA.
authors.forename: Mara
authors.initials: M
authors.lastname: Prentiss
mesh_terms: D004247:DNA / Q000378:metabolism; D003663:Decision Trees; D019277:Entropy; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D011938:Rec A Recombinases / Q000378:metabolism*; D017385:Sequence Homology; D013997:Time Factors
chemical_list: D004247:DNA; D011938:Rec A Recombinases