ArticleProceedings of the National Academy of Sciences of the United States of America2021
Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 23 citations in OpenAlex.
- Twist-encoded magnetic plasmon interferometry for label-free, orientation-resolved single-molecule imaging.Science advances · 2026Article
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Collective interactions along recombinase-bound D-loops could speed repair of double-strand breaks by destabilizing flanking homoduplex tails.Nucleic acids research · 2026Article
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- DNA topology: A central dynamic coordinator in chromatin regulation.Current opinion in structural biology · 2024Review
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- Structural and Dynamic Changes of Nucleosome upon GATA3 Binding.Journal of molecular biology · 2023Article
- Article
- Genome modeling: From chromatin fibers to genes.Current opinion in structural biology · 2023Review
- DNA methylation cues in nucleosome geometry, stability and unwrapping.Nucleic acids research · 2022Article
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Torsional stress has a significant impact on the structure and stability of the nucleosome. RNA polymerase imposes torsional stress on the DNA in chromatin and unwraps the DNA from the nucleosome to access the genetic information encoded in the DNA. To understand how the torsional stress affects the stability of the nucleosome, we examined the unwrapping of two half superhelical turns of nucleosomal DNA from either end of the DNA under torsional stress with all-atom molecular dynamics simulations. The free energies for unwrapping the DNA indicate that positive stress that overtwists DNA facilitates a large-scale asymmetric unwrapping of the DNA without a large extension of the DNA. During the unwrapping, one end of the DNA was dissociated from H3 and H2A-H2B, while the other end of the DNA stably remained wrapped. The detailed analysis indicates that this asymmetric dissociation is facilitated by the geometry and bendability of the DNA under positive stress. The geometry stabilized the interaction between the major groove of the twisted DNA and the H3 α
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