ArticleNucleic acids research2018
A coarse-grained model for DNA origami.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- DNA Origami and Their Application in Biosensors.Biosensors · 2026Review
- Isotopic H/D Exchange in Hydrogen Bonds Between the Nitrogenous Bases of the CAG Repeat Tract Makes It Possible to Stabilize Its Expansion in theBiomedicines · 2025Article
- Coarse-grained mathematical models for studying mechanical properties of the DNA.Biophysical reviews · 2025Review
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Application and prospects of nucleic acid nanomaterials in tumor therapy.RSC advances · 2023Review
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions.PLoS computational biology · 2022Article
- Disulfide Dimerization of Neuronal Calcium Sensor-1: Implications for Zinc and Redox Signaling.International journal of molecular sciences · 2021Article
- Integrated computer-aided engineering and design for DNA assemblies.Nature materials · 2021Article
- Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding.The journal of physical chemistry. B · 2021Article
- MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems.Nucleic acids research · 2020Article
- From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.Interface focus · 2019Review
- Coarse-grained modelling of the structural properties of DNA origami.Nucleic acids research · 2019Article
- Characterization of Hydroxyproline-Containing Hairpin-Like Antimicrobial Peptide EcAMP1-Hyp from Barnyard Grass (International journal of molecular sciences · 2018Article
- QM/MM Description of Newly Selected Catalytic Bioscavengers Against Organophosphorus Compounds Revealed Reactivation Stimulus Mediated by Histidine Residue in the Acyl-Binding Loop.Frontiers in pharmacology · 2018Article
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Authors and funding
8 authors.
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Abstract
Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.
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