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Site-directed placement of three-dimensional DNA origami

Nature Nanotechnology (2023)Cite this article

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Abstract

The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA–silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.

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Fig. 1: Assembly of 3D hybrid DNA–silica nanostructured substrates.
Fig. 2: Assembly of 3D hybrid nanostructured substrates by on-surface annealing of DNA origami nanotubes to a flat connector origami.
Fig. 3: Pattern diversity.
Fig. 4: Assembly of 3D hybrid nanostructured substrates by direct deposition.
Fig. 5: Assembly of hybrid silica–AuNPs–DNA nanostructures prepared via nanosphere lithography.

Data availability

The data that support the findings of this study are openly available in ref. 50. The data supporting the findings of this study are available within this article and its Supplementary Information.

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Acknowledgements

We thank C. Obermayer for cleanroom assistance and S. Kempter for assistance with TEM. Besides all the group members, we thank N. Vogel (FAU Erlangen-Nürnberg) for the helpful discussions. I.V.M., G.P., X.Y. and T.L. acknowledge funding from the ERC consolidator grant ‘DNA Funs’ (Project ID: 818635). E.E., V.R. and T.L. further acknowledge support from the cluster of excellence e-conversion EXC 2089/1-390776260. This work was funded by the Federal Ministry of Education and Research (BMBF) and the Free State of Bavaria under the Excellence Strategy of the Federal Government and the Länder through the ONE MUNICH Projects Munich Multiscale Biofabrication and Enabling Quantum Communication and Imaging Applications.

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Authors and Affiliations

  1. Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany

    Irina V. Martynenko, Elisabeth Erber, Veronika Ruider, Mihir Dass, Gregor Posnjak, Xin Yin, Philipp Altpeter & Tim Liedl

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  1. Irina V. Martynenko
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Contributions

T.L. and I.V.M. designed this study; they also designed the DNA origami samples as well as designed and optimized the interfaces. I.V.M., E.E. and V.R. assembled and purified the DNA origami samples. G.P. and X.Y. designed, assembled and purified the DNA origami tetrapods and 24HBs as well as designed the tetrapod–AuNPs and tetrapod–24HB interfaces. I.V.M., E.E. and V.R. performed the placement experiments, surface annealing experiments, AFM and SEM measurements and data analysis with assistance from M.D. and P.A. I.V.M. and T.L. wrote the paper with input from all authors.

Corresponding authors

Correspondence to Irina V. Martynenko or Tim Liedl.

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Nature Nanotechnology thanks Nayan Agarwal and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Notes 1–15, Figs. 1–44, Tables 1 and 2 and References.

Supplementary Table 1

DNA sequences in an Excel file.

Supplementary Data 1

The caDNAno origami designs in JSON files.

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Martynenko, I.V., Erber, E., Ruider, V. et al. Site-directed placement of three-dimensional DNA origami. Nat. Nanotechnol. (2023). https://doi.org/10.1038/s41565-023-01487-z

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