ArticleNature communications2021
Supercoiling and looping promote DNA base accessibility and coordination among distant sites.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 55 citations in OpenAlex.
- Mapping the Conformational Landscape of DNA Minicircles Through Atomic Force Microscopy and Shape Space Analysis.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- The eukaryotic homology search complex distorts donor DNA structure to probe for homology.Genes & development · 2026Article
- The interplay between supercoiling and DNA modifying enzymes at the single-molecule level.Scientific reports · 2026Article
- DNA deformability in sequence-dependent capture of E. coli gyrase.Nature communications · 2026Article
- DNA topological regulation in RNA polymerase II transcription.Cellular & molecular biology letters · 2026Review
- The molecular mechanisms of quinolone resistance in Salmonella: a review.Archives of microbiology · 2025Review
- A high-throughput single-molecule platform to study DNA supercoiling effect on protein-DNA interactions.Nucleic acids research · 2025Article
- Article
- A Water-Soluble Aggregation-Induced Emission Photosensitizer with Intrinsic Antibacterial Activity as an Antiplanktonic and Antibiofilm Therapeutic Agent.Journal of medicinal chemistry · 2025Article
- Centromeres are stress-induced fragile sites.Current biology : CB · 2025Article
- DNA packaging by molecular motors: from bacteriophage to human chromosomes.Nature reviews. Genetics · 2024Review
- DdrC, a unique DNA repair factor from D. radiodurans, senses and stabilizes DNA breaks through a novel lesion-recognition mechanism.Nucleic acids research · 2024Article
- Nanoscale Interaction of Endonuclease APE1 with DNA.International journal of molecular sciences · 2024Article
- Structural basis of DNA crossover capture byScience (New York, N.Y.) · 2024Article
- Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA.Nature communications · 2024Article
- The nucleolar shell provides anchoring sites for DNA untwisting.Communications biology · 2024Article
- Non-canonical DNA structures in the human ribosomal DNA.Histochemistry and cell biology · 2023Review
- Suitability of double-stranded DNA as a molecular standard for the validation of analytical ultracentrifugation instruments.European biophysics journal : EBJ · 2023Article
- DNA supercoiling-induced shapes alter minicircle hydrodynamic properties.Nucleic acids research · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
DNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.