ArticleNucleic acids research2021
The loopometer: a quantitative in vivo assay for DNA-looping proteins.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 7 citations in OpenAlex.
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- When push comes to shove - RNA polymerase and DNA-bound protein roadblocks.Biophysical reviews · 2023Review
- RNA polymerase efficiently transcribes through DNA-scaffolded, cooperative bacteriophage repressor complexes.FEBS letters · 2022Article
- DNA Bending Force Facilitates Z-DNA Formation under Physiological Salt Conditions.Journal of the American Chemical Society · 2022Article
- Single-molecule insights into torsion and roadblocks in bacterial transcript elongation.Transcription · 2021Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins that can bring together separate DNA sites, either on the same or on different DNA molecules, are critical for a variety of DNA-based processes. However, there are no general and technically simple assays to detect proteins capable of DNA looping in vivo nor to quantitate their in vivo looping efficiency. Here, we develop a quantitative in vivo assay for DNA-looping proteins in Escherichia coli that requires only basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, where two binding sites for the candidate looping protein are inserted internally to a pair of operators for the E. coli LacI repressor. DNA looping between the sites shortens the effective distance between the lac operators, increasing LacI looping and strengthening its repression of a lacZ reporter gene. Analysis based on a general model for loop assistance enables quantitation of the strength of looping conferred by the protein and its binding sites. We use this 'loopometer' assay to measure DNA looping for a variety of bacterial and phage proteins.
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Registered trials
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