ArticlePloS one2016
Supercoiling Effects on Short-Range DNA Looping in E. coli.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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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.
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.
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Who cites it
10 citing papers in PubMed, 13 citations in OpenAlex.
- Artificial repression looping control by regulated autoinhibition of transcription activator-like effector dimer proteins.Nucleic acids research · 2026Article
- Engineered transcription activator-like effector dimer proteins confer DNA loop-dependent gene repression comparable to Lac repressor.Nucleic acids research · 2024Article
- High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria.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
- Role of the Discriminator Sequence in the Supercoiling Sensitivity of Bacterial Promoters.mSystems · 2021Article
- Dependence of DNA looping onInternational journal of biochemistry and molecular biology · 2019Article
- Protein-mediated loops in supercoiled DNA create large topological domains.Nucleic acids research · 2018Article
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes.Genome biology and evolution · 2017Review
- Transcription control engineering and applications in synthetic biology.Synthetic and systems biotechnology · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades. Here we adapt this model to test the hypothesis that negative superhelical strain facilitates the formation of short-range (6-8 DNA turns) repression loops in E. coli. The natural negative superhelicity of E. coli DNA is regulated by the interplay of gyrase and topoisomerase enzymes, adding or removing negative supercoils, respectively. Here, we measured quantitatively DNA looping in three different E. coli strains characterized by different levels of global supercoiling: wild type, gyrase mutant (gyrB226), and topoisomerase mutant (ΔtopA10). DNA looping in each strain was measured by assaying repression of the endogenous lac operon, and repression of ten reporter constructs with DNA loop sizes between 70-85 base pairs. Our data are most simply interpreted as supporting the hypothesis that negative supercoiling facilitates gene repression by small DNA-protein loops in living bacteria.
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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.