FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling
mBio, 2020 DNA supercoiling (DS) is essential for life because it controls critical processes, including transcription, replication, and recombination. Current methods to measure DNA supercoiling in vivo are laborious and unable to examine single cells.
Alexandre Duprey, Eduardo A. Groisman
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DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling [PDF]
Frontiers in Microbiology, 2023 DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses
Ivan Junier +4 more
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DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines. [PDF]
PLoS Genetics, 2020 DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA. These
Alexandre Duprey, Eduardo A Groisman
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The bacterial promoter spacer modulates promoter strength and timing by length, TG-motifs and DNA supercoiling sensitivity [PDF]
Scientific Reports, 2021 Transcription, the first step to gene expression, is a central coordination process in all living matter. Besides a plethora of regulatory mechanisms, the promoter architecture sets the foundation of expression strength, timing and the potential for ...
Carlo A. Klein +3 more
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DNA supercoiling-mediated G4/R-loop formation tunes transcription by controlling the access of RNA polymerase [PDF]
Nature CommunicationsRNA polymerase (RNAP) is a processive motor that modulates DNA supercoiling and reshapes DNA structures. The feedback loop between the DNA topology and transcription remains elusive.
Jihee Hwang +8 more
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DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria? [PDF]
Computational and Structural Biotechnology Journal, 2019 DNA supercoiling acts as a global and ancestral regulator of bacterial gene expression. In this review, we advocate that it plays a pivotal role in host-pathogen interactions by transducing environmental signals to the bacterial chromosome and ...
Shiny Martis B. +4 more
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DNA supercoiling and transcription in bacteria: a two-way street [PDF]
BMC Molecular and Cell Biology, 2019 Background The processes of DNA supercoiling and transcription are interdependent because the movement of a transcription elongation complex simultaneously induces under- and overwinding of the DNA duplex and because the initiation, elongation and ...
Charles J. Dorman
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Counterintuitive DNA Sequence Dependence in Supercoiling-Induced DNA Melting.
PLoS ONE, 2015 The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins.
Rifka Vlijm, Jaco V D Torre, Cees Dekker
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HU of Streptococcus pneumoniae Is Essential for the Preservation of DNA Supercoiling [PDF]
Frontiers in Microbiology, 2018 The histone-like protein HU is a conserved nucleoid-associated protein that is involved in the maintenance of the bacterial chromosome architecture. It is the only known nucleoid-associated protein in Streptococcus pneumoniae, but it has not been studied.
María-José Ferrándiz +4 more
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Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time. [PDF]
Nucleic Acids Res, 2021 Yan Y +6 more
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