ArticleBiophysical journal2015
Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- Searching for sequence features that control DNA cyclizability.PNAS nexus · 2026Article
- Idea engines: Unifying innovation & obsolescence from markets & genetic evolution to science.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- 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
- Characterization of Gene Repression by Designed Transcription Activator-like Effector Dimer Proteins.Biophysical journal · 2020Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
- Thermal fracture kinetics of heterogeneous semiflexible polymers.Soft matter · 2020Article
- Role of nucleosome positioning in 3D chromatin organization and loop formation.Journal of biosciences · 2020Article
- Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking.Physical review letters · 2019Article
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- The free-energy cost of interaction between DNA loops.Scientific reports · 2017Article
- Buckling a Semiflexible Polymer Chain under Compression.Polymers · 2017Article
- Supercoiling biases the formation of loops involved in gene regulation.Biophysical reviews · 2016Review
- Single-molecule fluorescence studies on DNA looping.Methods (San Diego, Calif.) · 2016Article
- Protein-Assisted DNA Looping: A Delicate Balance among Interactions, Mechanics, and Entropy.Biophysical journal · 2015Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
DNA looping plays a key role in many fundamental biological processes, including gene regulation, recombination, and chromosomal organization. The looping of DNA is often mediated by proteins whose structural features and physical interactions can alter the length scale at which the looping occurs. Looping and unlooping processes are controlled by thermodynamic contributions associated with mechanical deformation of the DNA strand and entropy arising from thermal fluctuations of the conformation. To determine how these confounding effects influence DNA looping and unlooping kinetics, we present a theoretical model that incorporates the role of the protein interactions, DNA mechanics, and conformational entropy. We show that for shorter DNA strands the interaction distance affects the transition state, resulting in a complex relationship between the looped and unlooped state lifetimes and the physical properties of the looped DNA. We explore the range of behaviors that arise with varying interaction distance and DNA length. These results demonstrate how DNA deformation and entropy dictate the scaling of the looping and unlooping kinetics versus the J-factor, establishing the connection between kinetic and equilibrium behaviors. Our results show how the twist-and-bend elasticity of the DNA chain modulates the kinetics and how the influence of the interaction distance fades away at intermediate to longer chain lengths, in agreement with previous scaling predictions.
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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.