We investigated the possibility to measure DNA supercoiling density (\sigma) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, parS. We predict ParB clusters to be leaky, which actually hinders the precise measurementof \sigma. We propose avenues to circumvent this problem and present analyses demonstrating consistency between chromosomal and plasmid data {\it  {\it   .
We investigate the measurement of DNA supercoiling density (\sigma) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS . Using this framework, we provide an upper bound for \sigma in the{\it Escherichia coli chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries .
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investigated the possibility to measure
investigate the measurement of
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parS. We predict ParB clusters to be leaky, which actually hinders the precise measurementof \sigma. We propose avenues to circumvent this problem and present analyses demonstrating consistency between chromosomal and plasmid data
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parS
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. Using this framework, we provide an upper bound for \sigma in the
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Escherichia coli
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chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries