ArticleNucleic acids research2020
Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- 3D DNA origami-enabled molecularly addressable optical nanocircuit.Science advances · 2026Article
- A nanoscale Jitterbug transformer from DNA.Nature communications · 2026Article
- Cooperativity, entropy, and effective concentration in DNA origami self-replication.Science advances · 2026Article
- U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism.Nucleic acids research · 2026Article
- DNA Origami and Their Application in Biosensors.Biosensors · 2026Review
- In-Situ ssDNA Isolation from dsDNA Sources as a Streamlined Pathway to DNA Origami Assembly and Testing.bioRxiv : the preprint server for biology · 2026Article
- Breaking the stoichiometric limit of padlock probe ligation via catalytic hairpin assembly-and-cyclization.Nucleic acids research · 2026Article
- Self-Assembling RNA Nanostructures are Highly Sensitive to Environmental Conditions.Journal of molecular biology · 2026Article
- Coarse-Grained Modeling and Simulation of Multistranded RNA Nanostars.Chem & bio engineering · 2026Article
- High-speed 3D DNA PAINT and unsupervised clustering for unlocking 3D DNA origami cryptography.Nature communications · 2025Article
- Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures.Nature communications · 2025Article
- PyFuRNAce: an integrated design engine for RNA origami.Nature communications · 2025Article
- Disruption of the Nucleolin-CXCR4 interaction by the DNA aptamer HY-4 halts colorectal cancer metastasis.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Single-molecule capture, release, and dynamical manipulation via reversible electrokinetic confinement (RECON).Science advances · 2025Article
- Economical and Versatile Subunit Design Principles for Self-Assembled DNA Origami Structures.ACS nano · 2025Article
- Ballistic diffusion fronts in biomolecular condensates.Nature nanotechnology · 2025Article
- How We Simulate DNA Origami.Small methods · 2025Article
- Wireframe DNA Origami Capable of Vertex-protruding Transformation.Chembiochem : a European journal of chemical biology · 2025Article
- Automated design of scaffold-free DNA wireframe nanostructures.Nature communications · 2025Article
- Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells.Nature nanotechnology · 2025Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures.
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