ArticleProceedings of the National Academy of Sciences of the United States of America2010
Chemically accurate coarse graining of double-stranded DNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Article
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- Coarse-Grained Models to Study Protein-DNA Interactions and Liquid-Liquid Phase Separation.Journal of chemical theory and computation · 2024Article
- Coarse-Grained Modeling Using Neural Networks Trained on Structural Data.Journal of chemical theory and computation · 2023Article
- OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates.PLoS computational biology · 2023Article
- Anomalous Diffusion of Polyelectrolyte Segments on Supported Charged Lipid Bilayers.Entropy (Basel, Switzerland) · 2023Article
- OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates.bioRxiv : the preprint server for biology · 2023Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Mechanical Constraint Effect on DNA Persistence Length.Molecules (Basel, Switzerland) · 2022Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- On the stability and layered organization of protein-DNA condensates.Biophysical journal · 2022Article
- Single-stranded nucleic acid binding and coacervation by linker histone H1.Nature structural & molecular biology · 2022Article
- Bottom-Up Coarse-Grained Modeling of DNA.Frontiers in molecular biosciences · 2021Review
- A multiscale analysis of DNA phase separation: from atomistic to mesoscale level.Nucleic acids research · 2019Article
- Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.Biophysical journal · 2019Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Coarse-grained (CG) modeling approaches are widely used to simulate many important biological processes involving DNA, including chromatin folding and genomic packaging. The bending propensity of a semiflexible DNA molecule critically influences these processes. However, existing CG DNA models do not retain a sufficient fidelity of the important local chain motions, whose propagation at larger length scales would generate correct DNA persistent lengths, in particular when the solution's ionic strength is widely varied. Here we report on a development of an accurate CG model for the double-stranded DNA chain, with explicit treatment of mobile ions, derived systematically from all-atom molecular dynamics simulations. Our model generates complex local motions of the DNA chain, similar to fully atomistic dynamics, leading also to a quantitative agreement of our simulation results with the experimental data on the dependence of the DNA persistence length on the solution ionic strength. We also predict a structural transition in a torsionally stressed DNA nanocircle as the buffer ionic strength is increased beyond a threshold value.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.