ArticleNucleic acids research2015
Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Macromolecular crowding alters transcription: real-time measurements with SYBR Green II.Research square · 2026Article
- Review
- Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.Nature communications · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, and Stability of DNA.Sub-cellular biochemistry · 2025Review
- Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions.Chemical reviews · 2024Review
- Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures.Polymers · 2021Article
- Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids.Science advances · 2021Article
- Article
- Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling.Biophysical journal · 2020Article
- Chromosomal Organization and Regulation of Genetic Function inEcoSal Plus · 2020Article
- Brownian Dynamics Simulations of Biological Molecules.Trends in chemistry · 2019Article
- Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes.Nucleic acids research · 2018Article
- Probing hyper-negatively supercoiled mini-circles with nucleases and DNA binding proteins.PloS one · 2018Article
- Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe.Nucleic acids research · 2017Article
- Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.Nucleic acids research · 2017Article
- Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.Nucleic acids research · 2017Article
- Spatial confinement induces hairpins in nicked circular DNA.Nucleic acids research · 2017Article
- Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation.Biophysical journal · 2016Article
- How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation.Nucleic acids research · 2016Article
- Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.Nucleic acids research · 2015Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA-DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.
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