Letter | Published:

Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

Nature volume 552, pages 7277 (07 December 2017) | Download Citation


Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity1,2,3,4,5,6,7,8,9,10,11,12,13,14, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami4, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands6,7,10,11,12,13,14. Even larger DNA origami structures are possible15,16, but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock8,9. This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success9. Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1–1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can be produced within this molecular canvas, enabling the creation of shapes such as letters, a helicoid and a teddy bear. We anticipate that with further optimization of structure design, strand synthesis and assembly procedure even larger structures could be accessible, which could be useful for applications such as positioning functional components.

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We thank N. Ponnuswamy, R. Sørensen, J. Hahn, J. Lara, L. Chou, N. Garreau, S. Saka, H. Sasaki, J. B. Woehrstein and C. B. Marks for experimental help. We also thank B. Wei, W. Sun and W.M. Shih for discussions, M. Beatty and J. Cheng for help in developing the Nanobricks platform, and C. Chen for assistance with draft preparation. The work was funded by Office of Naval Research grants N000141010827, N000141310593, N000141410610, N000141612182 and N000141612410, an Army Research Office grant W911NF1210238, National Science Foundation grants CCF-1054898, CCF-1162459, CCF-1317291, CMMI-1333215, CMMI-1334109 and CMMI-1344915, an Air Force Office of Scientific Research grant AFA9550-15-1-0514, and National Institute of Health grants 1DP2OD007292 and 1R01EB018659, 167814 (P.Y.); an Emory Biomedical Engineering Department Startup Fund, an Emory Winship Cancer Institute Billi and Bernie Marcus Research Award, a Winship Cancer Institute grant number IRG-14-188-0 from the American Cancer Society, and a National Science Foundation CAREER Award DMR–1654485 (Y.K.); French National Research Agency grants ANR-16-CE09-0004-01 and ANR-15-CE09-0003-02 (G.B.); and a French National Research Agency grant ANR-10-INBS-05 (P.B.). L.L.O. was funded by an NSF graduate research fellowship. N.H. was funded by the German National Academic Foundation and German Academic Exchange Service. M.T.S. acknowledges support from the International Max Planck Research School for Molecular and Cellular Life Sciences (IMPRS-LS).

Author information


  1. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA

    • Luvena L. Ong
    • , Nikita Hanikel
    • , Omar K. Yaghi
    • , Casey Grun
    • , Maximilian T. Strauss
    • , Florian Schueder
    • , Bei Wang
    • , Jocelyn Y. Kishi
    • , Cameron Myhrvold
    • , Allen Zhu
    •  & Peng Yin
  2. Harvard–MIT Program in Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Luvena L. Ong
  3. Max Planck Institute of Biochemistry, 82152 Martinsried Munich, Germany

    • Maximilian T. Strauss
    • , Florian Schueder
    •  & Ralf Jungmann
  4. Department of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539 Munich, Germany

    • Maximilian T. Strauss
    • , Florian Schueder
    •  & Ralf Jungmann
  5. Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, F-34000 Montpellier, France

    • Patrick Bron
    •  & Josephine Lai-Kee-Him
  6. Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China

    • Bei Wang
  7. Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia 30322, USA

    • Pengfei Wang
    •  & Yonggang Ke
  8. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Jocelyn Y. Kishi
    • , Cameron Myhrvold
    •  & Peng Yin
  9. Institut de Génomique Fonctionnelle, CNRS UMR 5203, INSERM U1191, F-34000 Montpellier, France

    • Gaetan Bellot
  10. Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA

    • Yonggang Ke


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L.L.O. conceived the project, designed and performed the experiments, analysed the data and wrote the paper. N.H. designed and performed the experiments, analysed the data and wrote the paper. O.K.Y., B.W. and P.W. performed the experiments and analysed the data. M.T.S. and F.S. performed the 3D DNA-PAINT experiments, analysed the data and wrote the paper. C.G. and J.Y.K. developed the Nanobricks software and wrote the paper. P.B. and J.L.-K.-H. performed the electron tomography experiments. C.M. designed and analysed the sequencing experiments and wrote the paper. A.Z. performed the experiments. R.J. supervised the DNA-PAINT experiments, interpreted data and wrote the paper. G.B. designed and supervised the electron tomography study, interpreted data and wrote the paper. Y.K. and P.Y. conceived, designed and supervised the study, interpreted the data and wrote the paper.

Competing interests

A patent has been filed based on this work. P.Y. is co-founder of Ultivue Inc. and NuProbe Global.

Corresponding authors

Correspondence to Gaetan Bellot or Yonggang Ke or Peng Yin.

Reviewer Information Nature thanks C. Lin and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

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    Supplementary Information

    This file contains Supplementary Methods and Data, Supplementary Tables 1-3, Supplementary Figures 1-113 and Supplementary References – see contents pages for details.

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    Supplementary Data 1

    This file contains the sequences used for each structure on separate tabs.


  1. 1.

    Bear structure

    Tomography video of the bear structure

  2. 2.

    GEB structure

    Tomography video of the GEB structure

  3. 3.

    Helix structure

    Tomography video of the helix structure

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