ArticleNucleic acids research2020
MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems.
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 44 papers.
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Who cites it
44 citing papers in PubMed.
- Tetrahedral DNA Nanostructures: A Structural-Family-Aware Review from Computational Design and Biological Stability to Translational Nanomedicine.Nanomaterials (Basel, Switzerland) · 2026Review
- Expandable DNA-origami rings as a nanomechanical platform for studying disordered nucleoporins.bioRxiv : the preprint server for biology · 2026Article
- From Blueprint to Breakthrough: How Far Can We Fold DNA Origami for Nano-Enabled Technologies?JACS Au · 2026Review
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- DNA-Lipid Nanodiscs with a Polyethylene Glycol Interface.Journal of the American Chemical Society · 2026Article
- DNA Origami and Their Application in Biosensors.Biosensors · 2026Review
- SNUPI: A Computational Framework for Rapid Mechanical Analysis of Structured DNA Assemblies.JACS Au · 2025Article
- Chemical Composition and Backbone Modifications Define Deformability of Nucleic Acid Nanoparticles.ACS nano · 2025Article
- How We Simulate DNA Origami.Small methods · 2025Article
- Single-molecule dynamic structural biology with vertically arranged DNA on a fluorescence microscope.Nature methods · 2025Article
- A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport.Nature communications · 2024Article
- Nanopore Translocation Reveals Electrophoretic Force on Noncanonical RNA:DNA Double Helix.ACS nano · 2024Article
- Single molecule delivery into living cells.Nature communications · 2024Article
- Article
- A DNA turbine powered by a transmembrane potential across a nanopore.Nature nanotechnology · 2024Article
- Enzyme-Free Exponential Amplification via Growth and Scission of Crisscross Ribbons from Single-Stranded DNA Components.Journal of the American Chemical Society · 2024Article
- Replicating Chromosomes in Whole-Cell Models of Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A computational model for structural dynamics and reconfiguration of DNA assemblies.Nature communications · 2023Article
- Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids.The journal of physical chemistry. B · 2023Article
- Versatile computer-aided design of free-form DNA nanostructures and assemblies.Science advances · 2023Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.
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