Structural dynamics of nucleosomes at single-molecule resolution
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The detailed mechanisms of how DNA that is assembled around a histone core can be accessed by DNA-binding proteins for transcription, replication, or repair, remain elusive nearly 40 years after Kornberg's nucleosome model was proposed. Uncovering the structural dynamics of nucleosomes is a crucial step in elucidating the mechanisms regulating genome accessibility. This requires the deconvolution of multiple structural states within an ensemble. Recent advances in single-molecule methods enable unprecedented efficiency in examining subpopulation dynamics. In this review, we summarize studies of nucleosome structure and dynamics from single-molecule approaches and how they advance our understanding of the mechanisms that govern DNA transactions.
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RNA and DNA exist as conformational ensembles in freely diffusing states, crystals, nucleosomes, ribosomes, and spliceosomes.
“RNA and DNA also exist as conformational ensembles, no matter whether in freely diffusing state,540 in crystal,541 or in large nucleosomes,542 ribosomes, or spliceosomes.”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [542]
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Agrawal, T., Pal, S., & Rakshit, T. (2026) · Nano Letters · doi:10.1021/acs.nanolett.5c06488 · Cited by 2 · see citing works
Elastic model for dinucleosome structure and energy
Fatemi, H., Khodabandeh, F., & Mohammad-Rafiee, F. (2016) · Physical review. E · doi:10.1103/physreve.93.042409 · Cited by 2 · see citing works
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Nucleosome assembly and disassembly pathways in vitro
Hatakeyama, A., Shymko, Y., Hartmann, B., Retureau, R., Noguès, C., Pasi, M., & Buckle, M. (2022) · PLoS ONE · doi:10.1371/journal.pone.0267382 · Cited by 1 · see citing works
A one-dimensional statistical mechanics model for nucleosome positioning on genomic DNA
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- Authors
- Choy, J. S., & Lee, T.-H.
- Affiliations
- Stanford University (US)
- Pennsylvania State University (US)
- Corresponding author
- Choy, John S.
- Lee, Tae-Hee
- Venue
- Trends in Biochemical Sciences
- Publisher
- Elsevier BV
- Published
- 2012-10
- Volume
- 37
- Issue
- 10
- Pages
- 425-435
- ISSN
- 0968-0004 (ISSN-L)
- PMC
- PMC3669752
- OpenAlex
- W2023860198
- Cited by
- 27
- References
- 84
- Citations by year
- 2026: 1 · 2025: 1 · 2023: 2 · 2022: 3 · 2021: 1 · 2019: 3 · 2017: 2 · 2016: 7 · 2015: 6 · 2013: 1
- FWCI
- 0.20
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Trends in Biochemical Sciences (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM097286, GM097286)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
- Keywords
- nucleosome structure, nucleosome dynamics, histone core, DNA-binding proteins, DNA accessibility, genome accessibility, transcription, DNA replication, DNA repair
- MeSH terms
- DNA, DNA-Binding Proteins, Humans, Models, Molecular, Nucleic Acid Conformation, Nucleosomes
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