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 similar to 9-15 bases. In this work, we will show that as a result of entropic and enthalpic barriers, simultaneously testing all similar to 9-15 bases as separate individual units results in a longer overall searching time than testing them in groups and stages.