Meta-DNA structures

Abstract

DNA origami has emerged as a highly programmable method to construct customized objects and functional devices in the 10–100 nm scale. Scaling up the size of the DNA origami would enable many potential applications, which include metamaterial construction and surface-based biophysical assays. Here we demonstrate that a six-helix bundle DNA origami nanostructure in the submicrometre scale (meta-DNA) could be used as a magnified analogue of single-stranded DNA, and that two meta-DNAs that contain complementary ‘meta-base pairs’ can form double helices with programmed handedness and helical pitches. By mimicking the molecular behaviours of DNA strands and their assembly strategies, we used meta-DNA building blocks to form diverse and complex structures on the micrometre scale. Using meta-DNA building blocks, we constructed a series of DNA architectures on a submicrometre-to-micrometre scale, which include meta-multi-arm junctions, three-dimensional (3D) polyhedrons, and various 2D/3D lattices. We also demonstrated a hierarchical strand-displacement reaction on meta-DNA to transfer the dynamic features of DNA into the meta-DNA. This meta-DNA self-assembly concept may transform the microscopic world of structural DNA nanotechnology.

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Fig. 1: Design and characterization of dsM-DNA.
Fig. 2: M-junctions and M-DX structures.
Fig. 3: Self-folded, self-linked M-DNA structures and self-assembled 3D polyhedrons.
Fig. 4: Self-assembly of 1D, 2D and 3D M-DNA micrometre-scale structures based on the M-SST assembly strategy.
Fig. 5: M-DNA-based strand displacement.

Data availability

All the data are available within this paper and its Supplementary Information. All the data are also available from the corresponding authors upon request.

Code availability

The code used for the ox-DNA simulation is available from the corresponding authors upon request.

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Acknowledgements

The authors thank K. S. Kim, C. Lee and D.-N. Kim for the help of persistence length calculating. The authors thank D. Lowry for help with the TEM imaging and K. Lee for editing the paper. This work was financially supported by the US National Science Foundation, National Key R&D Program of China (2018YFA0902600), NSFC (21991134, 21834007, 21904060 and 21675167), the innovative research team of high-level local universities in Shanghai and the K. C. Wong Foundation at Shanghai Jiao Tong University.

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Authors

Contributions

G.Y., C.F. and H.Y. conceived the project. G.Y., T.P., F.W., S.J., L.L. and C.G. performed the research. H.L., E.P. and P.Š. performed the oxDNA simulation. X.J., X.L. and L.W. helped with the polyhedron silicification. G.Y., F.Z., Y.L., C.F. and H.Y. wrote the manuscript.

Corresponding authors

Correspondence to Chunhai Fan or Hao Yan.

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The authors declare no competing interests.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–100, Tables 1–80 and Sequences 1–6.

Supplementary Video 1

Dynamic animation of unwrapped ds-M-DNA of left-handed 660° design.

Supplementary Video 2

Dynamic animation of wrapped ds-M-DNA of left-handed 660° design.

Supplementary Video 3

Dynamic animation of unwrapped ds-M-DNA of right-handed 660° design.

Supplementary Video 4

Dynamic animation of wrapped ds-M-DNA of right-handed 660° design.

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Yao, G., Zhang, F., Wang, F. et al. Meta-DNA structures. Nat. Chem. (2020). https://doi.org/10.1038/s41557-020-0539-8

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