Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A primer to scaffolded DNA origami

Abstract

Molecular self-assembly with scaffolded DNA origami enables building custom-shaped nanometer-scale objects with molecular weights in the megadalton regime. Here we provide a practical guide for design and assembly of scaffolded DNA origami objects. We also introduce a computational tool for predicting the structure of DNA origami objects and provide information on the conditions under which DNA origami objects can be expected to maintain their structure.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Examples of objects built with scaffolded DNA origami.
Figure 2: The scaffolded DNA origami design concept.
Figure 3: Packing and cross-over spacing rules for multilayer DNA origami.
Figure 4: CanDo.
Figure 5: Thermal stability and resistance against nucleases of three multilayer scaffolded DNA origami test structures.
Figure 6: Step-by-step guide through molecular self-assembly with scaffolded DNA origami.

Similar content being viewed by others

Swarup Dey, Chunhai Fan, … Pengfei Zhan

References

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

    Article  CAS  Google Scholar 

  2. Lulu, Q. et al. Analogic China map constructed by DNA. Chin. Sci. Bull. 51, 2973–2976 (2006).

    Article  Google Scholar 

  3. 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).

    Article  CAS  Google Scholar 

  4. Andersen, E.S. et al. DNA origami design of dolphin-shaped structures with flexible tails. ACS Nano 2, 1213–1218 (2008).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Douglas, S.M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (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. Douglas, S.M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).

    Article  CAS  Google Scholar 

  10. Ke, Y. et al. Multi-layer DNA origami packed on a square lattice. J. Am. Chem. Soc. 131, 15903–15908 (2009).

    Article  CAS  Google Scholar 

  11. Pound, E., Ashton, J.R., Becerril, H.A. & Woolley, A.T. Polymerase chain reaction based scaffold preparation for the production of thin, branched DNA origami nanostructures of arbitrary sizes. Nano Lett. 9, 4302–4305 (2009).

    Article  CAS  Google Scholar 

  12. Endo, M., Hidaka, K., Kato, T., Namba, K. & Sugiyama, H. DNA prism structures constructed by folding of multiple rectangular arms. J. Am. Chem. Soc. 131, 15570–15571 (2009).

    Article  CAS  Google Scholar 

  13. Kuzuya, A. & Komiyama, M. Design and construction of a box-shaped 3D-DNA origami. Chem. Commun. (Camb.) 28, 4182–4184 (2009).

    Article  Google Scholar 

  14. Endo, M., Katsuda, Y., Hidaka, K. & Sugiyama, H. Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. J. Am. Chem. Soc. 132, 1592–1597 (2010).

    Article  CAS  Google Scholar 

  15. Endo, M., Sugita, T., Katsuda, Y., Hidaka, K. & Sugiyama, H. Programmed-assembly system using DNA jigsaw pieces. Chem. Eur. J. 16, 5362–5368 (2010).

    Article  CAS  Google Scholar 

  16. Liedl, T., Högberg, B., Tytell, J., Ingber, D.E. & Shih, W.M. Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat. Nanotechnol. 5, 520–524 (2010).

    Article  CAS  Google Scholar 

  17. Han, D., Pal, S., Liu, Y. & Yan, H. Folding and cutting DNA into reconfigurable topological nanostructures. Nat. Nanotechnol. 5, 712–717 (2010).

    Article  CAS  Google Scholar 

  18. Liu, W., Zhong, H., Wang, R. & Seeman, N.C. Crystalline two-dimensional DNA-origami arrays. Angew. Chem. Int. Edn. Engl. 50, 264–267 (2010).

    Article  Google Scholar 

  19. Saccà, B. et al. Orthogonal protein decoration of DNA origami. Angew. Chem. Int. Edn. Engl. 49, 9378–9383 (2010).

    Article  Google Scholar 

  20. Shih, W.M. & Lin, C. Knitting complex weaves with DNA origami. Curr. Opin. Struct. Biol. 20, 276–282 (2010).

    Article  CAS  Google Scholar 

  21. Nangreave, J., Han, D. & Yan, H. DNA origami: a history and current perspective. Curr. Opin. Chem. Biol. 14, 608–615 (2010).

    Article  CAS  Google Scholar 

  22. Kershner, R.J. et al. Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nat. Nanotechnol. 4, 557–561 (2009).

    Article  CAS  Google Scholar 

  23. Sharma, J. et al. Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffolds. J. Am. Chem. Soc. 130, 7820–7821 (2008).

    Article  CAS  Google Scholar 

  24. Stearns, L.A. et al. Template-directed nucleation and growth of inorganic nanoparticles on DNA scaffolds. Angew. Chem. Int. Edn. Engl. 48, 8494–8496 (2009).

    Article  CAS  Google Scholar 

  25. Kuzyk, A., Laitinen, K.T. & Törmä, P. DNA origami as a nanoscale template for protein assembly. Nanotechnology 20, 235305 (2009).

    Article  Google Scholar 

  26. Shen, W., Zhong, H., Neff, D. & Norton, M.L. NTA directed protein nanopatterning on DNA Origami nanoconstructs. J. Am. Chem. Soc. 131, 6660–6661 (2009).

    Article  CAS  Google Scholar 

  27. Kuzuya, A. et al. Precisely programmed and robust 2D streptavidin nanoarrays by using periodical nanometer-scale wells embedded in DNA origami assembly. Chembiochem 10, 1811–1815 (2009).

    Article  CAS  Google Scholar 

  28. Bui, H. et al. Programmable periodicity of Quantum Dot arrays with DNA origami nanotubes. Nano Lett. 10, 3367–3372 (2010).

    Article  CAS  Google Scholar 

  29. Pal, S., Deng, S., Ding, B., Yan, H. & Liu, Y. DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. Angew. Chem. Int. Edn. Engl. 15, 2700–2704 (2010).

    Article  Google Scholar 

  30. Hung, A.M. et al. Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nat. Nanotechnol. 5, 121–126 (2010).

    Article  CAS  Google Scholar 

  31. Steinhauer, C., Jungmann, R., Sobey, T.L., Simmel, F.C. & Tinnefeld, P. DNA origami as a nanoscopic ruler for super-resolution microscopy. Angew. Chem. Int. Edn. Engl. 48, 8870–8873 (2009).

    Article  CAS  Google Scholar 

  32. Voigt, N.V. et al. Single-molecule chemical reactions on DNA origami. Nat. Nanotechnol. 5, 200–203 (2010).

    Article  CAS  Google Scholar 

  33. Maune, H.T. et al. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nat. Nanotechnol. 5, 61–66 (2009).

    Article  Google Scholar 

  34. Seeman, N.C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982).

    Article  CAS  Google Scholar 

  35. Fu, T.J. & Seeman, N.C. DNA double-crossover molecules. Biochemistry 32, 3211–3220 (1993).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  37. Drew, H.R. et al. Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. USA 78, 2179–2183 (1981).

    Article  CAS  Google Scholar 

  38. Rothemund, P.W.K. et al. Design and characterization of programmable DNA nanotubes. J. Am. Chem. Soc. 126, 16344–16352 (2004).

    Article  CAS  Google Scholar 

  39. Gore, J. et al. DNA overwinds when stretched. Nature 442, 836–839 (2006).

    Article  CAS  Google Scholar 

  40. Bathe, K.J. Finite Element Procedures (Prentice Hall, 1996).

    Google Scholar 

  41. Pettersen, E.F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    Article  CAS  Google Scholar 

  42. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415 (2003).

    Article  CAS  Google Scholar 

  43. Kunitz, M. Crystalline desoxyribonuclease; isolation and general properties; spectrophotometric method for the measurement of desoxyribonuclease activity. J. Gen. Physiol. 33, 349–362 (1950).

    Article  CAS  Google Scholar 

  44. White, M.F., Giraud-Panis, M.J., Pöhler, J.R. & Lilley, D.M. Recognition and manipulation of branched DNA structure by junction-resolving enzymes. J. Mol. Biol. 269, 647–664 (1997).

    Article  CAS  Google Scholar 

  45. Kerr, C. & Sadowski, P.D. Gene 6 exonuclease of bacteriophage T7. II. Mechanism of the reaction. J. Biol. Chem. 247, 311–318 (1972).

    CAS  PubMed  Google Scholar 

  46. Little, J.W. Lambda exonuclease. Gene Amplif. Anal. 2, 135–145 (1981).

    CAS  PubMed  Google Scholar 

  47. Lehman, I.R. & Nussbaum, A.L. The deoxyribonucleases of Escherischia coli. V. On the the specificity of exonuclease I (phosphodiesterase). J. Biol. Chem. 239, 2628–2636 (1964).

    CAS  Google Scholar 

  48. Morgan, R.D. Mse I, a unique restriction endonuclease from Micrococcus species which recognizes 5′ T decreases TAA 3′. Nucleic Acids Res. 16, 3104 (1988).

    Article  CAS  Google Scholar 

  49. Högberg, B., Liedl, T. & Shih, W.M. Folding DNA origami from a double-stranded source of scaffold. J. Am. Chem. Soc. 9, 4302–4305 (2009).

    Google Scholar 

  50. Jungmann, R., Liedl, T., Sobey, T.L., Shih, W.M. & Simmel, F.C. Isothermal assembly of DNA origami structures using denaturing agents. J. Am. Chem. Soc. 130, 10062–10063 (2008).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Cluster for Integrated Protein Science Munich and a Hans-Fischer tenure track grant from Technische Universität München Institute for Advanced Study to H.D., an Alexander von Humboldt fellowship to C.E.C. and a stipend from the Technische Universität München graduate school “Materials at Complex Interfaces” (CompInt) to F.K. Cluster for Integrated Protein Science Munich and Technische Universität München Institute for Advanced Study are funded by the German Excellence Initiative, CompInt is funded by the Elite Network of the state of Bavaria. M.B. and D.K. are supported by Massachusetts Institute of Technology faculty start-up funds and a Samuel A. Goldblith Career Development Professorship awarded to M.B. We thank J. Altschuler and G. McGill for implementing the CanDo website, S. Douglas for discussions on caDNAno details, and P. Rothemund for contributing the AFM imaging protocol and for helpful comments.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hendrik Dietz.

Ethics declarations

Competing interests

A patent has been filed on behalf of the Massachusetts Institute of Technology and Dana Farber Cancer Institute by Ditthavong Mori & Steiner, P.C. listing M.B., D.K. and H.D. as co-inventors of CanDo.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Protocols 1–5, Supplementary Notes 1–2, Supplementary Methods (PDF 5185 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Castro, C., Kilchherr, F., Kim, DN. et al. A primer to scaffolded DNA origami. Nat Methods 8, 221–229 (2011). https://doi.org/10.1038/nmeth.1570

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth.1570

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing