ArticleNucleic acids research2010
Gene repression by minimal lac loops in vivo.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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
40 citing papers in PubMed, 59 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
- Fructose-1-kinase has pleiotropic roles inbioRxiv : the preprint server for biology · 2023Article
- DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.Nucleic acids research · 2023Article
- Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics.Biophysical journal · 2022Article
- Designed architectural proteins that tune DNA looping in bacteria.Nucleic acids research · 2021Article
- Supercoiling and looping promote DNA base accessibility and coordination among distant sites.Nature communications · 2021Article
- Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems.Nature communications · 2021Article
- Engineering of a Promoter Repressed by a Light-Regulated Transcription Factor inBiodesign research · 2021Article
- Decoding an organ regeneration switch by dissecting cardiac regeneration enhancers.Development (Cambridge, England) · 2020Article
- Characterization of Gene Repression by Designed Transcription Activator-like Effector Dimer Proteins.Biophysical journal · 2020Article
- In silico analysis of non-synonymous single nucleotide polymorphisms (nsSNPs) in the human GJA3 gene associated with congenital cataract.BMC molecular and cell biology · 2020Article
- Bacterial gene control by DNA looping using engineered dimeric transcription activator like effector (TALE) proteins.Nucleic acids research · 2018Article
- Development of inducer-free expression plasmids based on IPTG-inducible promoters for Bacillus subtilis.Microbial cell factories · 2017Article
- Tailor-made transcriptional biosensors for optimizing microbial cell factories.Journal of industrial microbiology & biotechnology · 2017Review
- Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects.Biophysical reviews · 2016Review
- Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects.Biophysical reviews · 2016Review
- Single-molecule fluorescence studies on DNA looping.Methods (San Diego, Calif.) · 2016Article
- Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope.FEBS letters · 2016Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The inflexibility of double-stranded DNA with respect to bending and twisting is well established in vitro. Understanding apparent DNA physical properties in vivo is a greater challenge. Here, we exploit repression looping with components of the Escherichia coli lac operon to monitor DNA flexibility in living cells. We create a minimal system for testing the shortest possible DNA repression loops that contain an E. coli promoter, and compare the results to prior experiments. Our data reveal that loop-independent repression occurs for certain tight operator/promoter spacings. When only loop-dependent repression is considered, fits to a thermodynamic model show that DNA twisting limits looping in vivo, although the apparent DNA twist flexibility is 2- to 4-fold higher than in vitro. In contrast, length-dependent resistance to DNA bending is not observed in these experiments, even for the shortest loops constraining <0.4 persistence lengths of DNA. As observed previously for other looping configurations, loss of the nucleoid protein heat unstable (HU) markedly disables DNA looping in vivo. Length-independent DNA bending energy may reflect the activities of architectural proteins and the structure of the DNA topological domain. We suggest that the shortest loops are formed in apical loops rather than along the DNA plectonemic superhelix.
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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.