ArticleNucleic acids research2019
Coarse-grained modelling of the structural properties of DNA origami.
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 42 papers.
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Who cites it
42 citing papers in PubMed.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- Multiscale Conformational Dynamics of DNA Holliday Junctions Modulated by Ion Concentration: Insights from Fluorescence Correlation Spectroscopy and Time-Resolved Anisotropy.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Tunable DNA Origami Nanosensors for Detection of Multiscale Spatial Ion Concentration Gradients.ACS sensors · 2026Article
- Coarse-Grained Modeling and Simulation of Multistranded RNA Nanostars.Chem & bio engineering · 2026Article
- SNUPI: A Computational Framework for Rapid Mechanical Analysis of Structured DNA Assemblies.JACS Au · 2025Article
- Tunable DNA Origami Nanosensors for Detection of Multiscale Spatial Ion Concentration Gradients.bioRxiv : the preprint server for biology · 2025Article
- Analyzing DNA Origami Nanostructure Assembly by Dynamic Light Scattering and Nanoparticle Tracking Analysis.Small methods · 2025Article
- How We Simulate DNA Origami.Small methods · 2025Article
- Visualizing Reactive Oxygen Species-Induced DNA Damage Process in Higher-Ordered Origami Nanostructures.JACS Au · 2025Article
- Bimodal DNA self-origami material with nucleic acid function enhancement.Journal of nanobiotechnology · 2024Article
- A computational model for structural dynamics and reconfiguration of DNA assemblies.Nature communications · 2023Article
- Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies.Nature communications · 2023Article
- Versatile computer-aided design of free-form DNA nanostructures and assemblies.Science advances · 2023Article
- DNA-Origami Line-Actants Control Domain Organization and Fission in Synthetic Membranes.Journal of the American Chemical Society · 2023Article
- Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking.Biophysical journal · 2022Article
- Mechanical deformation behaviors and structural properties of ligated DNA crystals.Biophysical journal · 2022Article
- Planar 2D wireframe DNA origami.Science advances · 2022Article
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5 authors.
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Abstract
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Å, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.
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