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

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.

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Figure 1: Three-dimensional nanostructures self-assembled from DNA bricks.
Figure 2: Self-assembly of brick cuboids.
Figure 3: Cavity shapes formed from a 30H × 30H × 260B molecular canvas.
Figure 4: Electron tomography analysis and computational 3D reconstruction of DNA brick structures.
Figure 5: DNA sequencing analysis of the teddy bear cavity structure.

References

  1. 1

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

    ADS  CAS  Article  Google Scholar 

  2. 2

    Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Shih, W. M., Quispe, J. D. & Joyce, G. F. A. 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618–621 (2004)

    ADS  CAS  Article  Google Scholar 

  4. 4

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

    ADS  CAS  Article  Google Scholar 

  5. 5

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

    ADS  CAS  Article  Google Scholar 

  6. 6

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

    ADS  CAS  Article  Google Scholar 

  7. 7

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

    ADS  CAS  Article  Google Scholar 

  8. 8

    Wei, B., Dai, M. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–626 (2012)

    ADS  CAS  Article  Google Scholar 

  9. 9

    Ke, Y., Ong, L. L., Shih, W. M. & Yin, P. Three-dimensional structures self-assembled from DNA bricks. Science 338, 1177–1183 (2012)

    ADS  CAS  Article  Google Scholar 

  10. 10

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

    ADS  CAS  Article  Google Scholar 

  11. 11

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

    ADS  CAS  Article  Google Scholar 

  12. 12

    Gerling, T., Wagenbauer, K. F., Neuner, A. M. & Dietz, H. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components. Science 347, 1446–1452 (2015)

    ADS  CAS  Article  Google Scholar 

  13. 13

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

    ADS  CAS  Article  Google Scholar 

  14. 14

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

    ADS  CAS  Article  Google Scholar 

  15. 15

    Marchi, A. N., Saaem, I., Vogen, B. N., Brown, S. & Labean, T. H. Towards larger DNA origami. Nano Lett. 14, 5740–5747 (2014)

    ADS  CAS  Article  Google Scholar 

  16. 16

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

    CAS  Article  Google Scholar 

  17. 17

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

    CAS  Article  Google Scholar 

  18. 18

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

    CAS  Article  Google Scholar 

  19. 19

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

    CAS  Article  Google Scholar 

  20. 20

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

    CAS  Article  Google Scholar 

  21. 21

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

    ADS  CAS  Article  Google Scholar 

  22. 22

    Jacobs, W. M., Reinhardt, A. & Frenkel, D. Rational design of self-assembled pathways for complex multicomponent structures. Proc. Natl Acad. Sci. USA 112, 6313–6318 (2015)

    ADS  CAS  Article  Google Scholar 

  23. 23

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

    ADS  CAS  Article  Google Scholar 

  24. 24

    Douglas, S. M., Chou, J. J. & Shih, W. M. DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc. Natl Acad. Sci. USA 104, 6644–6648 (2007)

    ADS  CAS  Article  Google Scholar 

  25. 25

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

    ADS  CAS  Article  Google Scholar 

  26. 26

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

    Article  Google Scholar 

  27. 27

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

    ADS  CAS  Article  Google Scholar 

  28. 28

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

    ADS  CAS  Article  Google Scholar 

  29. 29

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

    ADS  CAS  Article  Google Scholar 

  30. 30

    Rajendran, A., Endo, M., Katsuda, Y., Hidaka, K. & Sugiyama, H. Programmed two-dimensional self-assembly of multiple DNA origami jigsaw pieces. ACS Nano 5, 665–671 (2011)

    CAS  Article  Google Scholar 

  31. 31

    Sobczak, J.-P. J., Martin, T. G., Gerling, T. & Dietz, H. Rapid folding of DNA into nanoscale shapes at constant temperature. Science 338, 1458–1461 (2012)

    ADS  CAS  Article  Google Scholar 

  32. 32

    Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012)

    CAS  Article  Google Scholar 

  33. 33

    Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008)

    ADS  CAS  Article  Google Scholar 

  34. 34

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

    CAS  Article  Google Scholar 

  35. 35

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

    CAS  Article  Google Scholar 

  36. 36

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

    CAS  Article  Google Scholar 

  37. 37

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

    CAS  Article  Google Scholar 

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

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Authors

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.

Corresponding authors

Correspondence to Gaetan Bellot or Yonggang Ke or Peng Yin.

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Competing interests

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

Additional information

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

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Extended data figures and tables

Extended Data Figure 1 Gel electrophoresis analysis of DNA brick cuboids.

ah, Structures of varying size (see schematics on the left) were assembled isothermally for 5–7 days at the temperatures indicated above each gel lane, with strand concentrations of 30 nM (ad), 5 nM (e, g), 3 nM (f) and 20 nM (h). The number below each lane indicates the formation yield of the target structure. Lane ‘M’ contains a 1-kilobase ladder.

Extended Data Figure 2 Characterization of 30H × 30H × 260B cavity shapes.

a, Schematic of the 30H × 30H × 260B molecular canvas (grey) compared with a DNA-origami-sized structure (blue). b, For each structure (numbered 1–7), the top panels show 3D models of the designed structure, the bottom left panels show expected TEM projections and the bottom right panels show the TEM averages from at least six particles. c, The structures were folded with 5 nM per strand by isothermal annealing or by using a narrow ramp from 52.5 °C to 51 °C. Products were analysed on a 0.5% agarose gel in the presence of 10 mM MgCl2. The percentage listed below a target band indicates the gel yield; labels correspond to those in b or in Fig. 3.

Supplementary information

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. (PDF 30485 kb)

Supplementary Data 1

This file contains the sequences used for each structure on separate tabs. (XLSX 4706 kb)

Bear structure

Tomography video of the bear structure (AVI 11680 kb)

GEB structure

Tomography video of the GEB structure (AVI 12801 kb)

Helix structure

Tomography video of the helix structure (AVI 7636 kb)

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Ong, L., Hanikel, N., Yaghi, O. et al. Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components. Nature 552, 72–77 (2017). https://doi.org/10.1038/nature24648

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