ArticleProceedings of the National Academy of Sciences of the United States of America2014
Modulation of DNA loop lifetimes by the free energy of loop formation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 30 citations in OpenAlex.
- Robustness of DNA looping across multiple cell divisions in individual bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.Biophysical journal · 2022Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
- Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model.Journal of chemical theory and computation · 2019Article
- Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking.Physical review letters · 2019Article
- Comparison between Effects of Retroactivity and Resource Competition upon Change in Downstream Reporter Genes of Synthetic Genetic Circuits.Life (Basel, Switzerland) · 2019Article
- Measurement of Mesoscale Conformational Dynamics of Freely Diffusing Molecules with Tracking FCS.Biophysical journal · 2018Article
- The free-energy cost of interaction between DNA loops.Scientific reports · 2017Article
- Buckling a Semiflexible Polymer Chain under Compression.Polymers · 2017Article
- Article
- Aspects of protein-DNA interactions: a review of quantitative thermodynamic theory for modelling synthetic circuits utilising LacI and CI repressors, IPTG and the reporter gene lacZ.Biophysical reviews · 2016Review
- Single-molecule fluorescence studies on DNA looping.Methods (San Diego, Calif.) · 2016Article
- Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.Biophysical journal · 2015Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for transcriptional regulation in both prokaryotes and eukaryotes, and the speed of such regulations affects the fitness of individuals. Here, we examine the in vitro looping dynamics of the classic Lac repressor gene-regulatory motif. We show that both loop association and loop dissociation at the DNA-repressor junctions depend on the elastic deformation of the DNA and protein, and that both looping and unlooping rates approximately scale with the looping J factor, which reflects the system's deformation free energy. We explain this observation by transition state theory and model the DNA-protein complex as an effective worm-like chain with twist. We introduce a finite protein-DNA binding interaction length, in competition with the characteristic DNA deformation length scale, as the physical origin of the previously unidentified loop dissociation dynamics observed here, and discuss the robustness of this behavior to perturbations in several polymer parameters.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.