Recently, DNA has been used to make nanodevices for a myriad of applications across fields including medicine, nanomanufacturing, synthetic biology, biosensing and biophysics. However, current DNA nanodevices rely primarily on geometric design, and it remains challenging to rationally design functional properties such as force-response or actuation behaviour. Here we report an iterative design pipeline for DNA assemblies that integrates computer-aided engineering based on coarse-grained molecular dynamics with a versatile computer-aided design approach that combines top-down automation with bottom-up control over geometry. This intuitive framework allows for rapid construction of large, multicomponent assemblies from three-dimensional models with finer control over the geometrical, mechanical and dynamical properties of the DNA structures in an automated manner. This approach expands the scope of structural complexity and enhances mechanical and dynamic design of DNA assemblies.
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Original data for TEM images and gel electrophoresis are included as Source data. The remaining data supporting the findings of this study are available within the Article and its supplementary information files or available from the corresponding author upon reasonable request.
The developed design software MagicDNA is available from GitHub at https://github.com/cmhuang2011/MagicDNA.
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This work was supported by National Science Foundation (NSF) grant 1536862 to H.-J.S. and C.E.C. and grant 1921881 to C.E.C. We acknowledge F. Engelhardt and H. Dietz for providing custom scaffolds, T. Aksel and S. Douglas for sharing the caDNAno toolkit, C. Maffeo and A. Aksimentiev for supporting the interface to MrDNA, T. MacCulloch and N. Stephanopoulos for providing K10 peptide and A. Tran, P. Le and P. Lukeman for testing MagicDNA Runtime packages. We thank the Campus Microscopy and Imaging Facility (CMIF) of The Ohio State University for imaging support. We also thank W. Pfeifer and C. Maffeo for critiques on the manuscript and supplementary material. Funding provided by NSF (NSF CMMI) 1536862 and NSF (NSF CMMI) 1921881.
The authors declare no competing interests.
Peer review information Nature Materials thanks Ebbe Andersen and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Supplementary Notes 1–3, Figs. 1–87, Table 1, captions for Videos 1 and 2, and References 1–27.
Top-down parametric design for a hinge structure performed by converting two lines into bundles and specifying the connectivity to assemble the components.
The final design profile of the airplane and the CG simulation with 3 × 108 steps.
The Excel sheets for the staple list of the 14 structures for fabrication.
Unprocessed gels and gel-intensity analysis for yield determination.
MagicDNA design file and unprocessed TEM image.
DNA origami structure raw TEM images.
Source data for motion analysis of 4 bar mechanism.
DNA origami structure raw TEM images.
DNA origami structure raw TEM images.
DNA origami structure raw TEM images and gel electrophoresis image depicting robot arm assembly.
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Huang, CM., Kucinic, A., Johnson, J.A. et al. Integrated computer-aided engineering and design for DNA assemblies. Nat. Mater. 20, 1264–1271 (2021). https://doi.org/10.1038/s41563-021-00978-5
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