ArticleScientific reports2017
Order and interactions in DNA arrays: Multiscale molecular dynamics simulation.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Helical correlations in curved DNA condensates.Nucleic acids research · 2025Article
- Impact of Divalent Cations on In-Layer Positional Order of DNA-Based Liquid Crystals: Implications for DNA Condensation.Biomacromolecules · 2024Article
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- From adaptive resolution to molecular dynamics of open systems.The European physical journal. B · 2021Review
- Additive Modulation of DNA-DNA Interactions by Interstitial Ions.Biophysical journal · 2020Article
- Multivalent counterions induced attraction between DNA polyelectrolytes.RSC advances · 2020Article
- SWINGER: a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids.Interface focus · 2019Review
- Sticking and stacking: Persistent ordering of fragmented DNA analogs.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution.Biophysical journal · 2018Article
- Electric Field of DNA in Solution: Who Is in Charge?Physical review. XArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.
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