ArticleNucleic acids research2012
DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 29 citations in OpenAlex.
- Tethered Particle Motion Analysis of DNA-Binding Properties of Architectural Proteins.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI.Nucleic acids research · 2023Article
- Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.Nucleic acids research · 2020Article
- Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics.Methods in enzymology · 2017Article
- A novel arrangement of zinc finger nuclease system for in vivo targeted genome engineering: the tomato LEC1-LIKE4 gene case.Plant cell reports · 2016Article
- Simulation of DNA Supercoil Relaxation.Biophysical journal · 2016Article
- Optical Pushing: A Tool for Parallelized Biomolecule Manipulation.Biophysical journal · 2016Article
- Prediction of fine-tuned promoter activity from DNA sequence.F1000Research · 2016Article
- Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.Biophysical journal · 2015Article
- Modulation of DNA loop lifetimes by the free energy of loop formation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Repetitive sequence variations in the promoter region of the adhesin-encoding gene sabA of Helicobacter pylori affect transcription.Journal of bacteriology · 2014Article
- Type II restriction endonucleases--a historical perspective and more.Nucleic acids research · 2014Review
- Enhanced tethered-particle motion analysis reveals viscous effects.Biophysical journal · 2014Article
- Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.Nucleic acids research · 2014Article
- Rationally designed coiled-coil DNA looping peptides control DNA topology.Nucleic acids research · 2013Article
- Measuring shape-dependent looping probability of DNA.Biophysical journal · 2013Article
- Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level.International journal of molecular sciences · 2013Article
- Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA.Nucleic acids research · 2013Article
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
Abstract
Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a 'torsional' catch bond.
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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.