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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.

The loopometer: a quantitative in vivo assay for DNA-looping proteins