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Meta-DNA structures

Nature Chemistry volume 12, pages 1067–1075 (2020)Cite this article

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An Author Correction to this article was published on 24 November 2020

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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.

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Article 28 January 2021

Swarup Dey, Chunhai Fan, … Pengfei Zhan

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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Author notes

  1. These authors contributed equally: Guangbao Yao, Fei Zhang, Fei Wang.

Authors and Affiliations

  1. School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China

    Guangbao Yao, Fei Wang, Xinxin Jing, Xiaoguo Liu & Chunhai Fan

  2. School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA

    Guangbao Yao, Fei Zhang, Hao Liu, Erik Poppleton, Petr Šulc, Shuoxing Jiang, Lan Liu, Chen Gong, Yan Liu & Hao Yan

  3. Department of Chemistry, Rutgers University-Newark, Newark, NJ, USA

    Fei Zhang

  4. Joint Research Center for Precision Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital South Campus, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China

    Fei Wang

  5. Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China

    Tianhuan Peng

  6. Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China

    Lihua Wang

  7. Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China

    Lihua Wang

  8. Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China

    Chunhai Fan

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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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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. 12, 1067–1075 (2020). https://doi.org/10.1038/s41557-020-0539-8

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