ArticleNucleic acids research2009
Dissecting protein-induced DNA looping dynamics in real time.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Tethered Particle Motion Analysis of DNA-Binding Properties of Architectural Proteins.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Detecting DNA Loops Using Tethered Particle Motion.Methods in molecular biology (Clifton, N.J.) · 2024Article
- 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
- Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination.Micromachines · 2018Review
- Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization.Scientific reports · 2016Article
- Optical Pushing: A Tool for Parallelized Biomolecule Manipulation.Biophysical journal · 2016Article
- DNA recognition by Escherichia coli CbpA protein requires a conserved arginine-minor-groove interaction.Nucleic acids research · 2015Article
- Acoustic force spectroscopy.Nature methods · 2015Article
- Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins.Biochemistry · 2014Article
- TPM analyses reveal that FtsK contributes both to the assembly and the activation of the XerCD-dif recombination synapse.Nucleic acids research · 2014Article
- 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
- DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.Nucleic acids research · 2012Article
- DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations.Nucleic acids research · 2012Article
- Article
- Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A.Nature communications · 2012Article
- Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region.Biophysical journal · 2011Article
- Gene repression by minimal lac loops in vivo.Nucleic acids research · 2010Article
- DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme.Nucleic acids research · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Many proteins that interact with DNA perform or enhance their specific functions by binding simultaneously to multiple target sites, thereby inducing a loop in the DNA. The dynamics and energies involved in this loop formation influence the reaction mechanism. Tethered particle motion has proven a powerful technique to study in real time protein-induced DNA looping dynamics while minimally perturbing the DNA-protein interactions. In addition, it permits many single-molecule experiments to be performed in parallel. Using as a model system the tetrameric Type II restriction enzyme SfiI, that binds two copies of its recognition site, we show here that we can determine the DNA-protein association and dissociation steps as well as the actual process of protein-induced loop capture and release on a single DNA molecule. The result of these experiments is a quantitative reaction scheme for DNA looping by SfiI that is rigorously compared to detailed biochemical studies of SfiI looping dynamics. We also present novel methods for data analysis and compare and discuss these with existing methods. The general applicability of the introduced techniques will further enhance tethered particle motion as a tool to follow DNA-protein dynamics in real time.
Indexed as
Identifiers
What OpenQuestion holds
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.