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Folding and cutting DNA into reconfigurable topological nanostructures

Abstract

Topology is the mathematical study of the spatial properties that are preserved through the deformation, twisting and stretching of objects. Topological architectures are common in nature and can be seen, for example, in DNA molecules that condense and relax during cellular events1. Synthetic topological nanostructures, such as catenanes and rotaxanes, have been engineered using supramolecular chemistry, but the fabrication of complex and reconfigurable structures remains challenging2. Here, we show that DNA origami3 can be used to assemble a Möbius strip, a topological ribbon-like structure that has only one side4,5,6. In addition, we show that the DNA Möbius strip can be reconfigured through strand displacement7 to create topological objects such as supercoiled ring and catenane structures. This DNA fold-and-cut strategy, analogous to Japanese kirigami8, may be used to create and reconfigure programmable topological structures that are unprecedented in molecular engineering.

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Figure 1: Design of a Möbius DNA strip.
Figure 2: Visualization of the Möbius DNA strips with AFM and TEM imaging.
Figure 3: DNA kirigami to achieve reconfigurable topologies from the Möbius strip.

References

  1. Bates, A. D. & Maxwell, A. DNA Topology 2nd edn (Oxford Univ. Press, 2005).

  2. Sauvage, J. P. & Dietrich-Buchecker, C. (eds) Molecular Catenane, Rotaxanes and Knots: A Journey through the World of Molecular Topology (Wiley-VCH, 1999).

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

    CAS  Article  Google Scholar 

  4. Starostin, E. L. & Van Der Heijden, G. H. M. The shape of a Möbius strip. Nature Mater. 6, 563–567 (2007).

    CAS  Article  Google Scholar 

  5. Yoon, Z. S., Osuka, A. & Kim, D. Möbius aromaticity and antiaromaticity in expanded porphyrins. Nature Chem. 1, 113–122 (2009).

    CAS  Article  Google Scholar 

  6. Lukin, O. & Vögtle, F. Knotting and threading of molecules: chemistry and chirality of molecular knots and their assemblies. Angew. Chem. Int. Ed. 44, 1456–1477 (2005).

    CAS  Article  Google Scholar 

  7. Yurke, B., Turberfield, A. J., Mills, A. P., Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).

    CAS  Article  Google Scholar 

  8. Rutzky, J. Kirigami: Exquisite Projects to Fold and Cut (Metro Books, 2007).

  9. Seeman, N. C. DNA in a material world. Nature 421, 427–431 (2003).

    Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  11. Lin, C., Liu, Y. & Yan, H. Designer DNA nanoarchitectures. Biochemistry 48, 1663–1674 (2009).

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  14. Goodman, R. P. et al. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310, 1661–1665 (2005).

    CAS  Article  Google Scholar 

  15. He, Y. et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198–U141 (2008).

    CAS  Article  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).

    CAS  Article  Google Scholar 

  17. Andersen, E. S. et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73–76 (2009).

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  19. Ke, Y. et al. Scaffolded DNA origami of a DNA tetrahedron molecular container. Nano Lett. 9, 2445–2447 (2009).

    CAS  Article  Google Scholar 

  20. Kuzuya, A. & Komiyama, M. Design and construction of a box-shaped 3D-DNA origami. Chem. Commun. 4182–4184 (2009).

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

    CAS  Article  Google Scholar 

  22. Ke, Y., Lindsay, S., Chang, Y., Liu, Y. & Yan, H. Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 319, 180–183 (2008).

    CAS  Article  Google Scholar 

  23. Rinker, S., Ke, Y., Liu, Y., Chhabra, R. & Yan, H. Self-assembled DNA nanostructures for distance-dependent multivalent ligand–protein binding. Nature Nanotech. 3, 418–422 (2008).

    CAS  Article  Google Scholar 

  24. Voigt, N. V. et al. Single-molecule chemical reactions on DNA origami. Nature Nanotech. 5, 200–203 (2010).

    CAS  Article  Google Scholar 

  25. Ding, B. et al. Gold nanoparticles' self-similar chain structure organized by DNA origami. J. Am. Chem. Soc. 132, 3248–3249 (2010).

    CAS  Article  Google Scholar 

  26. Pal, S., Deng, Z., Ding, B., Yan, H. & Liu, Y. DNA origami directed self-assembly of discrete silver nanoparticle architectures. Angew. Chem. Int. Ed. 49, 2700–2704 (2010).

    CAS  Article  Google Scholar 

  27. Chichak, K. S. et al. Molecular Borromean rings. Science 304, 1308–1312 (2004).

    CAS  Article  Google Scholar 

  28. Faiz, J. A., Heitz, V. & Sauvage, J.-P. Design and synthesis of porphyrin-containing catenanes and rotaxanes. Chem. Soc. Rev. 38, 422–442 (2009).

    CAS  Article  Google Scholar 

  29. Du, S. M., Stollar, B. D. & Seeman, N. C. A synthetic DNA molecule in three knotted topologies. J. Am. Chem. Soc. 117, 1194–1200 (1995).

    CAS  Article  Google Scholar 

  30. Mao, C., Sun, W. & Seeman, N. C. Construction of Borromean rings from DNA. Nature 386, 137–138 (1997).

    CAS  Article  Google Scholar 

  31. Ackermann, D. et al. A double stranded DNA rotaxane. Nature Nanotech. 5, 436–442 (2010).

    CAS  Article  Google Scholar 

  32. Sharma, J. et al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323, 112–116 (2009).

    CAS  Article  Google Scholar 

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Acknowledgements

The authors acknowledge financial support from the Office of Naval Research, Army Research Office, National Science Foundation, National Institute of Health and Department of Energy to H.Y. and Y.L., and the Alfred P. Sloan Fellowship to H.Y. Y.L. and H.Y. were also supported as part of the Center for Bio-Inspired Solar Fuel Production, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under award no. DE-SC0001016. The authors acknowledge use of the EM facility in the School of Life Sciences at Arizona State University. The authors also thank C. Flores for help in proofreading the manuscript.

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H.Y. and D.H. conceived and designed the experiment. D.H., S.P. and Y.L. performed the experiments. D.H., Y.L., S.P. and H.Y. analysed the data. All authors discussed the results. H.Y., Y.L. and D.H. wrote the manuscript.

Corresponding authors

Correspondence to Yan Liu or Hao Yan.

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The authors declare no competing financial interests.

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Han, D., Pal, S., Liu, Y. et al. Folding and cutting DNA into reconfigurable topological nanostructures. Nature Nanotech 5, 712–717 (2010). https://doi.org/10.1038/nnano.2010.193

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