ArticlePloS one2009
Concentration and length dependence of DNA looping in transcriptional regulation.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 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
61 citing papers in PubMed, 94 citations in OpenAlex.
- 3D Genome Engineering Using CRISPR/dCas Systems.International journal of molecular sciences · 2026Review
- Competition between glycine and GABAProceedings of the National Academy of Sciences of the United States of America · 2025Article
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
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- mRNA initiation and termination are spatially coordinated.bioRxiv : the preprint server for biology · 2024Article
- Detecting DNA Loops Using Tethered Particle Motion.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.Biophysical journal · 2022Article
- DNAcycP: a deep learning tool for DNA cyclizability prediction.Nucleic acids research · 2022Article
- Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability.Molecules and cells · 2022Review
- Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time.Nucleic acids research · 2021Article
- Article
- Deciphering the regulatory genome ofeLife · 2020Article
- Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination.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
- Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination.Micromachines · 2018Review
- Measurement of Mesoscale Conformational Dynamics of Freely Diffusing Molecules with Tracking FCS.Biophysical journal · 2018Article
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Insights into Genome Architecture Deduced from the Properties of Short Lac Repressor-mediated DNA Loops.Biophysical reviews · 2016Article
- Pseudomonas aeruginosa AmrZ Binds to Four Sites in the algD Promoter, Inducing DNA-AmrZ Complex Formation and Transcriptional Activation.Journal of bacteriology · 2016Article
1 more citing papers are in PubMed but not listed here.
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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage), to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least) two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping.
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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.