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Versatile computer-aided design of free-form DNA nanostructures and assemblies

Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables design of complex 3D DNA assemblies with man...

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Autores principales: Pfeifer, Wolfgang G., Huang, Chao-Min, Poirier, Michael G., Arya, Gaurav, Castro, Carlos E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10371015/
https://www.ncbi.nlm.nih.gov/pubmed/37494445
http://dx.doi.org/10.1126/sciadv.adi0697
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author Pfeifer, Wolfgang G.
Huang, Chao-Min
Poirier, Michael G.
Arya, Gaurav
Castro, Carlos E.
author_facet Pfeifer, Wolfgang G.
Huang, Chao-Min
Poirier, Michael G.
Arya, Gaurav
Castro, Carlos E.
author_sort Pfeifer, Wolfgang G.
collection PubMed
description Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables design of complex 3D DNA assemblies with many components; however, the design of structures with free-form features like vertices or curvature still required iterative design guided by simulation feedback and user intuition. Here, we present an updated design tool, MagicDNA 2.0, that automates the design of free-form 3D geometries, leveraging design models informed by coarse-grained molecular dynamics simulations. Our GUI-based, stepwise design approach integrates a high level of automation with versatile control over assembly and subcomponent design parameters. We experimentally validated this approach by fabricating a range of DNA origami assemblies with complex free-form geometries, including a 3D Nozzle, G-clef, and Hilbert and Trifolium curves, confirming excellent agreement between design input, simulation, and structure formation.
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spelling pubmed-103710152023-07-27 Versatile computer-aided design of free-form DNA nanostructures and assemblies Pfeifer, Wolfgang G. Huang, Chao-Min Poirier, Michael G. Arya, Gaurav Castro, Carlos E. Sci Adv Physical and Materials Sciences Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables design of complex 3D DNA assemblies with many components; however, the design of structures with free-form features like vertices or curvature still required iterative design guided by simulation feedback and user intuition. Here, we present an updated design tool, MagicDNA 2.0, that automates the design of free-form 3D geometries, leveraging design models informed by coarse-grained molecular dynamics simulations. Our GUI-based, stepwise design approach integrates a high level of automation with versatile control over assembly and subcomponent design parameters. We experimentally validated this approach by fabricating a range of DNA origami assemblies with complex free-form geometries, including a 3D Nozzle, G-clef, and Hilbert and Trifolium curves, confirming excellent agreement between design input, simulation, and structure formation. American Association for the Advancement of Science 2023-07-26 /pmc/articles/PMC10371015/ /pubmed/37494445 http://dx.doi.org/10.1126/sciadv.adi0697 Text en Copyright © 2023 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license (https://creativecommons.org/licenses/by-nc/4.0/) , which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.
spellingShingle Physical and Materials Sciences
Pfeifer, Wolfgang G.
Huang, Chao-Min
Poirier, Michael G.
Arya, Gaurav
Castro, Carlos E.
Versatile computer-aided design of free-form DNA nanostructures and assemblies
title Versatile computer-aided design of free-form DNA nanostructures and assemblies
title_full Versatile computer-aided design of free-form DNA nanostructures and assemblies
title_fullStr Versatile computer-aided design of free-form DNA nanostructures and assemblies
title_full_unstemmed Versatile computer-aided design of free-form DNA nanostructures and assemblies
title_short Versatile computer-aided design of free-form DNA nanostructures and assemblies
title_sort versatile computer-aided design of free-form dna nanostructures and assemblies
topic Physical and Materials Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10371015/
https://www.ncbi.nlm.nih.gov/pubmed/37494445
http://dx.doi.org/10.1126/sciadv.adi0697
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