ArticlePhysical review. E, Statistical, nonlinear, and soft matter physics2014
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.
Article in Physical review. E, Statistical, nonlinear, and soft matter physics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Modeling the Homologous Recombination Process: Methods, Successes and Challenges.International journal of molecular sciences · 2023Review
- Predicting a Kind of Unusual Multiple-States Dimerization-Modes Transformation in Protein PD-L1 System by Computational Investigation and a Generalized Rate Theory.Frontiers in chemistry · 2021Article
- Mismatch sensing by nucleofilament deciphers mechanism of RecA-mediated homologous recombination.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A change of view: homologous recombination at single-molecule resolution.Nature reviews. Genetics · 2018Review
- ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences.Nucleic acids research · 2017Article
- Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA.PLoS computational biology · 2017Article
- ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex.The Journal of biological chemistry · 2016Article
- RecA: Regulation and Mechanism of a Molecular Search Engine.Trends in biochemical sciences · 2016Review
- DNA Sequence Alignment during Homologous Recombination.The Journal of biological chemistry · 2016Review
- Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure.Nucleic acids research · 2015Article
- The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo.Nucleic acids research · 2015Article
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Authors and funding
2 authors at 1 institution in 1 country.
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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.
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