Letter

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

Received:
Accepted:
Published online:

Abstract

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.

  • Subscribe to Nature for full access:

    $199

    Subscribe

Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.

References

  1. 1.

    & The synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–633 (1991)

  2. 2.

    , , & Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998)

  3. 3.

    , & 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618–621 (2004)

  4. 4.

    Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006)

  5. 5.

    et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009)

  6. 6.

    et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009)

  7. 7.

    et al. DNA origami with complex curvatures in three-dimensional space. Science 332, 342–346 (2011)

  8. 8.

    , & Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–626 (2012)

  9. 9.

    , , & Three-dimensional structures self-assembled from DNA bricks. Science 338, 1177–1183 (2012)

  10. 10.

    et al. DNA gridiron nanostructures based on four-arm junctions. Science 339, 1412–1415 (2013)

  11. 11.

    et al. Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science 344, 65–69 (2014)

  12. 12.

    , , & Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components. Science 347, 1446–1452 (2015)

  13. 13.

    et al. DNA rendering of polyhedral meshes at the nanoscale. Nature 523, 441–444 (2015)

  14. 14.

    et al. Designer nanoscale DNA assemblies programmed from the top down. Science 352, 1534 (2016)

  15. 15.

    , , , & Towards larger DNA origami. Nano Lett. 14, 5740–5747 (2014)

  16. 16.

    et al. DNA origami structures directly assembled from intact bacteriophages. Small 10, 1765–1769 (2014)

  17. 17.

    , & Self-assembly of symmetric finite-size DNA nanoarrays. J. Am. Chem. Soc. 127, 17140–17141 (2005)

  18. 18.

    et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11, 313–318 (2014)

  19. 19.

    et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009)

  20. 20.

    & 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography. Ultramicroscopy 96, 413–431 (2003)

  21. 21.

    et al. Barcode extension for analysis and reconstruction of structures (BEARS). Nat. Commun. 8, 14698 (2017)

  22. 22.

    , & Rational design of self-assembled pathways for complex multicomponent structures. Proc. Natl Acad. Sci. USA 112, 6313–6318 (2015)

  23. 23.

    et al. Molecular force spectroscopy with a DNA origami-based nanoscopic force clamp. Science 354, 305–307 (2016)

  24. 24.

    , & DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc. Natl Acad. Sci. USA 104, 6644–6648 (2007)

  25. 25.

    et al. Multi-enzyme complexes on DNA scaffolds capable of substrate channeling with an artificial swinging arm. Nat. Nanotechnol. 9, 531–536 (2014)

  26. 26.

    et al. Casting inorganic structures with DNA molds. Science 346, 1258361 (2014)

  27. 27.

    et al. Routing of individual polymers in designed patterns. Nat. Nanotechnol. 10, 892–898 (2015)

  28. 28.

    et al. Fluorescence enhancement at docking sites of DNA-directed self-assembled nanoantennas. Science 338, 506–510 (2012)

  29. 29.

    et al. Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries. Nat. Commun. 6, 8634 (2015)

  30. 30.

    , , , & Programmed two-dimensional self-assembly of multiple DNA origami jigsaw pieces. ACS Nano 5, 665–671 (2011)

  31. 31.

    , , & Rapid folding of DNA into nanoscale shapes at constant temperature. Science 338, 1458–1461 (2012)

  32. 32.

    , & NIH image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012)

  33. 33.

    , , & Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008)

  34. 34.

    et al. Sub-micrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat. Chem. 4, 832–839 (2012)

  35. 35.

    & ViSP: representing single-particle localizations in three dimensions. Nat. Methods 10, 689–690 (2013)

  36. 36.

    et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012)

  37. 37.

    et al. A large genome centre’s improvements to the Illumina sequencing system. Nat. Methods 5, 1005–1010 (2008)

Download references

Acknowledgements

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

Affiliations

  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

Authors

  1. Search for Luvena L. Ong in:

  2. Search for Nikita Hanikel in:

  3. Search for Omar K. Yaghi in:

  4. Search for Casey Grun in:

  5. Search for Maximilian T. Strauss in:

  6. Search for Patrick Bron in:

  7. Search for Josephine Lai-Kee-Him in:

  8. Search for Florian Schueder in:

  9. Search for Bei Wang in:

  10. Search for Pengfei Wang in:

  11. Search for Jocelyn Y. Kishi in:

  12. Search for Cameron Myhrvold in:

  13. Search for Allen Zhu in:

  14. Search for Ralf Jungmann in:

  15. Search for Gaetan Bellot in:

  16. Search for Yonggang Ke in:

  17. Search for Peng Yin in:

Contributions

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

PDF files

  1. 1.

    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.

Excel files

  1. 1.

    Supplementary Data 1

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

Videos

  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

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.