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Complex wireframe DNA origami nanostructures with multi-arm junction vertices

Nature Nanotechnology volume 10, pages 779–784 (2015)Cite this article

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Abstract

Structural DNA nanotechnology1,2,3,4 and the DNA origami technique5, in particular, have provided a range of spatially addressable two- and three-dimensional nanostructures6,7,8,9,10. These structures are, however, typically formed of tightly packed parallel helices5,6,7,8,9. The development of wireframe structures10,11 should allow the creation of novel designs with unique functionalities, but engineering complex wireframe architectures with arbitrarily designed connections between selected vertices in three-dimensional space remains a challenge. Here, we report a design strategy for fabricating finite-size wireframe DNA nanostructures with high complexity and programmability. In our approach, the vertices are represented by n × 4 multi-arm junctions (n = 2–10) with controlled angles, and the lines are represented by antiparallel DNA crossover tiles12 of variable lengths. Scaffold strands are used to integrate the vertices and lines into fully assembled structures displaying intricate architectures. To demonstrate the versatility of the technique, a series of two-dimensional designs including quasi-crystalline patterns and curvilinear arrays or variable curvatures, and three-dimensional designs including a complex snub cube and a reconfigurable Archimedean solid were constructed.

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Figure 1: Design principles.
Figure 2: Scaffold folding paths and representative AFM images for the simple Platonic tiling.
Figure 3: Scaffold folding path and representative AFM images for intricate 2D patterns.
Figure 4: 3D wireframe Archimedean solid structures.

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References

  1. Aldaye, F. A., Palmer, A. L. & Sleiman, H. F. Assembling materials with DNA as the guide. Science 321, 1795–1799 (2008).

    Article  CAS  Google Scholar 

  2. Seeman, N. C. Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65–87 (2010).

    Article  CAS  Google Scholar 

  3. Pinheiro, A. V., Han, D. R., Shih, W. M. & Yan, H. Challenges and opportunities for structural DNA nanotechnology. Nature Nanotech. 6, 763–772 (2011).

    Article  CAS  Google Scholar 

  4. Zhang, F., Nangreave, J., Liu, Y. & Yan, H. Structural DNA nanotechnology: state of the art and future perspective. J. Am. Chem. Soc. 136, 11198–11211 (2014).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Andersen, E. S. et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73–75 (2009).

    Article  CAS  Google Scholar 

  8. Dietz, H., Douglas, S. M. & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725–730 (2009).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  11. He, Y. et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198–201 (2008).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  13. West, D. B. Introduction to Graph Theory (Prentice Hall, 1996).

    Google Scholar 

  14. Gibbons, A. Algorithmic Graph Theory (Cambridge Univ. Press, 1985).

    Google Scholar 

  15. He, Y., Chen, Y., Liu, H., Ribbe, A. E. & Mao, C. Self-assembly of hexagonal DNA two-dimensional (2D) arrays. J. Am. Chem. Soc. 127, 12202–12203 (2005).

    Article  CAS  Google Scholar 

  16. Yan, H., Park, S. H., Finkelstein, G., Reif, J. H. & LaBean, T. H. DNA templated self-assembly of protein arrays and highly conductive nanowires. Science 301, 1882–1884 (2003).

    Article  CAS  Google Scholar 

  17. He, Y., Tian, Y., Ribbe, A. E. & Mao, C. D. Highly connected two-dimensional crystals of DNA six-point-stars. J. Am. Chem. Soc. 128, 15978–15979 (2006).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  19. Sommerville, D. M. Y. Introduction to the Geometry of N Dimensions (E. P. Dutton, 1929).

    Google Scholar 

  20. Wells, A. F. Three-Dimensional Nets and Polyhedra (Wiley, 1977).

    Google Scholar 

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

    Article  CAS  Google Scholar 

  22. Zhang, Y. & Seeman, N. C. Consruction of a DNA-truncated octahedron. J. Am. Chem. Soc. 116, 1661–1669 (1994).

    Article  CAS  Google Scholar 

  23. Yan, H., Zhang, X., Shen, Z. & Seeman, N. C. A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002).

    Article  CAS  Google Scholar 

  24. Kato, T., Goodman, R. P., Erben, C. M., Turberfield, A. J. & Namba, K. High-resolution structural analysis of a DNA nanostructure by cryoEM. Nano Lett. 9, 2747–2750 (2009).

    Article  CAS  Google Scholar 

  25. Shen, Z., Yan, H., Wang, T. & Seeman, N. C. Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology. J. Am. Chem. Soc. 126, 1666–1674 (2004).

    Article  CAS  Google Scholar 

  26. Geary, C., Rothemund, P. W. K. & Andersen, E. S. A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 345, 799–804 (2014).

    Article  CAS  Google Scholar 

  27. Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software for high resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999).

    Article  CAS  Google Scholar 

  28. Goddard, T. D., Huang, C. C. & Ferrin, T. E. Visualizing density maps with UCSF Chimera. J. Struct. Biol. 157, 281–287 (2007).

    Article  CAS  Google Scholar 

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Acknowledgements

This research was partly supported by grants to H.Y. and Y.L. from the National Science Foundation (nos. 1360635 and 1334109), the Army Research Office (no. W911NF-12-1-0420) and the National Institutes of Health (no. R01GM104960). H.Y. was supported by the Presidential Strategic Initiative Fund from Arizona State University. The authors thank M. Madjidi for proofreading.

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Authors and Affiliations

  1. The Biodesign Institute and the Department of Chemistry and Biochemistry, Center for Molecular Design and Biomimetics, Arizona State University, Tempe, 85287, Arizona, USA

    Fei Zhang, Shuoxing Jiang, Yan Liu & Hao Yan

  2. Department of Chemistry, Purdue University, West Lafayette, 47907, Indiana, USA

    Siyu Wu, Yulin Li & Chengde Mao

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  1. Fei Zhang
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  2. Shuoxing Jiang
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  6. Yan Liu
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  7. Hao Yan
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Contributions

H.Y., Y.L. and F.Z. conceived and designed the experiment. F.Z., S.J., S.W. and Y.L. performed the experiments. F.Z., S.J., S.W. and Y.L. analysed the data. All authors discussed the results. All authors contributed to the writing the manuscript.

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Correspondence to Yan Liu or Hao Yan.

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The authors declare no competing financial interests.

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Zhang, F., Jiang, S., Wu, S. et al. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nature Nanotech 10, 779–784 (2015). https://doi.org/10.1038/nnano.2015.162

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