ArticleNucleic acids research2016
Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics.
Article in Nucleic acids research, 2016. 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, 44 citations in OpenAlex.
- Pervasive RNA-binding protein enrichment on TAD boundaries regulates TAD organization.Nucleic acids research · 2025Article
- What tunes guanine ionization potential in a nucleosome? An all-in-one systematic QM/MM assessment.Biophysical journal · 2024Article
- Sequence Dependence in Nucleosome Dynamics.The journal of physical chemistry. B · 2024Article
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF.Computational and structural biotechnology journal · 2022Article
- Nucleosomal embedding reshapes the dynamics of abasic sites.Scientific reports · 2020Article
- Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding.Biophysical journal · 2020Article
- Autoimmunity and SLE: Factual and Semantic Evidence-Based Critical Analyses of Definitions, Etiology, and Pathogenesis.Frontiers in immunology · 2020Review
- The role of histone tails in nucleosome stability: An electrostatic perspective.Computational and structural biotechnology journal · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules.Nucleic acids research · 2019Article
- Molecular Mechanism of Spontaneous Nucleosome Unraveling.Journal of molecular biology · 2019Article
- Article
- Mechanical evolution of DNA double-strand breaks in the nucleosome.PLoS computational biology · 2018Article
- Nanoscale dynamics of centromere nucleosomes and the critical roles of CENP-A.Nucleic acids research · 2018Article
- Probing hyper-negatively supercoiled mini-circles with nucleases and DNA binding proteins.PloS one · 2018Article
- In silico evidence for sequence-dependent nucleosome sliding.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Article
- Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations.Nucleus (Austin, Tex.) · 2016Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA-core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA-core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome.
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