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

Publication ,  Journal Article
Pfeifer, WG; Huang, C-M; Poirier, MG; Arya, G; Castro, CE
Published in: Science advances
July 2023

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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Published In

Science advances

DOI

EISSN

2375-2548

ISSN

2375-2548

Publication Date

July 2023

Volume

9

Issue

30

Start / End Page

eadi0697

Related Subject Headings

  • Nucleic Acid Conformation
  • Nanotechnology
  • Nanostructures
  • Molecular Dynamics Simulation
  • DNA
  • Computer-Aided Design
 

Citation

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Pfeifer, W. G., Huang, C.-M., Poirier, M. G., Arya, G., & Castro, C. E. (2023). Versatile computer-aided design of free-form DNA nanostructures and assemblies. Science Advances, 9(30), eadi0697. https://doi.org/10.1126/sciadv.adi0697
Pfeifer, Wolfgang G., Chao-Min Huang, Michael G. Poirier, Gaurav Arya, and Carlos E. Castro. “Versatile computer-aided design of free-form DNA nanostructures and assemblies.Science Advances 9, no. 30 (July 2023): eadi0697. https://doi.org/10.1126/sciadv.adi0697.
Pfeifer WG, Huang C-M, Poirier MG, Arya G, Castro CE. Versatile computer-aided design of free-form DNA nanostructures and assemblies. Science advances. 2023 Jul;9(30):eadi0697.
Pfeifer, Wolfgang G., et al. “Versatile computer-aided design of free-form DNA nanostructures and assemblies.Science Advances, vol. 9, no. 30, July 2023, p. eadi0697. Epmc, doi:10.1126/sciadv.adi0697.
Pfeifer WG, Huang C-M, Poirier MG, Arya G, Castro CE. Versatile computer-aided design of free-form DNA nanostructures and assemblies. Science advances. 2023 Jul;9(30):eadi0697.

Published In

Science advances

DOI

EISSN

2375-2548

ISSN

2375-2548

Publication Date

July 2023

Volume

9

Issue

30

Start / End Page

eadi0697

Related Subject Headings

  • Nucleic Acid Conformation
  • Nanotechnology
  • Nanostructures
  • Molecular Dynamics Simulation
  • DNA
  • Computer-Aided Design