ArticleNucleic acids research2019
A multiscale analysis of DNA phase separation: from atomistic to mesoscale level.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 37 citations in OpenAlex.
- Translational Entropy-Driven Competitive and Additive Effects on DNA Higher-Order Structure via Ion Exchange Between Cations of Different Valencies.Entropy (Basel, Switzerland) · 2026Review
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.Biophysical journal · 2026Review
- Abundant positively-charged proteins underlie JCVI-Syn3A's expanded nucleoid and ribosome distribution.PLoS computational biology · 2026Article
- Helical correlations in curved DNA condensates.Nucleic acids research · 2025Article
- Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles.Biophysical journal · 2024Article
- Article
- Macrophage-Derived Extracellular DNA Initiates Heterotopic Ossification.Inflammation · 2023Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions.Journal of chemical theory and computation · 2022Article
- Extracellular DNA: A Missing Link in the Pathogenesis of Ectopic Mineralization.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Control of Chromatin Organization and Chromosome Behavior during the Cell Cycle through Phase Separation.International journal of molecular sciences · 2021Review
- Bottom-Up Coarse-Grained Modeling of DNA.Frontiers in molecular biosciences · 2021Review
- Coarse-grained Simulations of the Impact of Chain Length and Stiffness on the Formation and Aggregation of Polyelectrolyte Complexes.Macromolecular theory and simulations · 2020Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA condensation and phase separation is of utmost importance for DNA packing in vivo with important applications in medicine, biotechnology and polymer physics. The presence of hexagonally ordered DNA is observed in virus capsids, sperm heads and in dinoflagellates. Rigorous modelling of this process in all-atom MD simulations is presently difficult to achieve due to size and time scale limitations. We used a hierarchical approach for systematic multiscale coarse-grained (CG) simulations of DNA phase separation induced by the three-valent cobalt(III)-hexammine (CoHex3+). Solvent-mediated effective potentials for a CG model of DNA were extracted from all-atom MD simulations. Simulations of several hundred 100-bp-long CG DNA oligonucleotides in the presence of explicit CoHex3+ ions demonstrated aggregation to a liquid crystalline hexagonally ordered phase. Following further coarse-graining and extraction of effective potentials, we conducted modelling at mesoscale level. In agreement with electron microscopy observations, simulations of an 10.2-kb-long DNA molecule showed phase separation to either a toroid or a fibre with distinct hexagonal DNA packing. The mechanism of toroid formation is analysed in detail. The approach used here is based only on the underlying all-atom force field and uses no adjustable parameters and may be generalised to modelling chromatin up to chromosome size.
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