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A primer to scaffolded DNA origami

Abstract

Molecular self-assembly with scaffolded DNA origami enables building custom-shaped nanometer-scale objects with molecular weights in the megadalton regime. Here we provide a practical guide for design and assembly of scaffolded DNA origami objects. We also introduce a computational tool for predicting the structure of DNA origami objects and provide information on the conditions under which DNA origami objects can be expected to maintain their structure.

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Figure 1: Examples of objects built with scaffolded DNA origami.
Figure 2: The scaffolded DNA origami design concept.
Figure 3: Packing and cross-over spacing rules for multilayer DNA origami.
Figure 4: CanDo.
Figure 5: Thermal stability and resistance against nucleases of three multilayer scaffolded DNA origami test structures.
Figure 6: Step-by-step guide through molecular self-assembly with scaffolded DNA origami.

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Acknowledgements

This work was supported by the Cluster for Integrated Protein Science Munich and a Hans-Fischer tenure track grant from Technische Universität München Institute for Advanced Study to H.D., an Alexander von Humboldt fellowship to C.E.C. and a stipend from the Technische Universität München graduate school “Materials at Complex Interfaces” (CompInt) to F.K. Cluster for Integrated Protein Science Munich and Technische Universität München Institute for Advanced Study are funded by the German Excellence Initiative, CompInt is funded by the Elite Network of the state of Bavaria. M.B. and D.K. are supported by Massachusetts Institute of Technology faculty start-up funds and a Samuel A. Goldblith Career Development Professorship awarded to M.B. We thank J. Altschuler and G. McGill for implementing the CanDo website, S. Douglas for discussions on caDNAno details, and P. Rothemund for contributing the AFM imaging protocol and for helpful comments.

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Correspondence to Hendrik Dietz.

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A patent has been filed on behalf of the Massachusetts Institute of Technology and Dana Farber Cancer Institute by Ditthavong Mori & Steiner, P.C. listing M.B., D.K. and H.D. as co-inventors of CanDo.

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Supplementary Figures 1–5, Supplementary Protocols 1–5, Supplementary Notes 1–2, Supplementary Methods (PDF 5185 kb)

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Castro, C., Kilchherr, F., Kim, DN. et al. A primer to scaffolded DNA origami. Nat Methods 8, 221–229 (2011). https://doi.org/10.1038/nmeth.1570

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