ArticleNucleic acids research2015
A novel hybrid single molecule approach reveals spontaneous DNA motion in the nucleosome.
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 41 papers.
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Who cites it
41 citing papers in PubMed.
- Chromatin remodelling: a driving force in reverse mechanotransduction.RNA biology · 2026Review
- Three-color single-molecule fluorescence resonance energy transfer to study macromolecular dynamics.Current opinion in structural biology · 2026Review
- Conformations of Linker Histone H1 Bound to Nucleosome Arrays.Journal of molecular biology · 2026Article
- Roles of histone chaperone Nap1 and histone acetylation in regulating phase-separation of nucleosome arrays.Nature communications · 2025Article
- A Method for Constructing Nucleosome Arrays with Spatially Defined Histone PTMs and DNA Damage.Angewandte Chemie (International ed. in English) · 2025Article
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis.The Journal of chemical physics · 2025Article
- Nucleosome wrapping states encode principles of 3D genome organization.Nature communications · 2025Article
- Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis.bioRxiv : the preprint server for biology · 2024Article
- CENP-A and CENP-B collaborate to create an open centromeric chromatin state.Nature communications · 2023Article
- Methods to investigate nucleosome structure and dynamics with single-molecule FRET.Methods (San Diego, Calif.) · 2023Article
- The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics.Nucleic acids research · 2023Article
- Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome.Frontiers in molecular biosciences · 2023Article
- The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response.Genes · 2022Review
- Molecular dynamics simulations reveal how H3K56 acetylation impacts nucleosome structure to promote DNA exposure for lesion sensing.DNA repair · 2021Article
- Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.Nature communications · 2021Article
- Histone dynamics mediate DNA unwrapping and sliding in nucleosomes.Nature communications · 2021Article
- Reconstitution and Purification of Nucleosomes with Recombinant Histones and Purified DNA.Current protocols in molecular biology · 2020Article
- DNA Sequence Is a Major Determinant of Tetrasome Dynamics.Biophysical journal · 2019Article
- Physical Chemistry of Epigenetics: Single-Molecule Investigations.The journal of physical chemistry. B · 2019Review
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4 authors.
Funding
Abstract
Structural dynamics of nucleic acid and protein is an important physical basis of their functions. These motions are often very difficult to synchronize and too fast to be clearly resolved with the currently available single molecule methods. Here we demonstrate a novel hybrid single molecule approach combining stochastic data analysis with fluorescence correlation that enables investigations of sub-ms unsynchronized structural dynamics of macromolecules. Based on the method, we report the first direct evidence of spontaneous DNA motions at the nucleosome termini. The nucleosome, comprising DNA and a histone core, is the fundamental packing unit of eukaryotic genes that must be accessed during various genome transactions. Spontaneous DNA opening at the nucleosome termini has long been hypothesized to enable gene access in the nucleosome, but has yet to be directly observed. Our approach reveals that DNA termini in the nucleosome open and close repeatedly at 0.1-1 ms(-1). The kinetics depends on salt concentration and DNA-histone interactions but not much on DNA sequence, suggesting that this dynamics is universal and imposes the kinetic limit to gene access. These results clearly demonstrate that our method provides an efficient and robust means to investigate unsynchronized structural changes of DNA at a sub-ms time resolution.
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