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.

  • Letter
  • Published:

Self-assembly of a nanoscale DNA box with a controllable lid

Nature volume 459, pages 73–76 (2009)Cite this article

Abstract

The unique structural motifs and self-recognition properties of DNA can be exploited to generate self-assembling DNA nanostructures of specific shapes using a ‘bottom-up’ approach1. Several assembly strategies have been developed for building complex three-dimensional (3D) DNA nanostructures2,3,4,5,6,7,8. Recently, the DNA ‘origami’ method was used to build two-dimensional addressable DNA structures of arbitrary shape9 that can be used as platforms to arrange nanomaterials with high precision and specificity9,10,11,12,13. A long-term goal of this field has been to construct fully addressable 3D DNA nanostructures14,15. Here we extend the DNA origami method into three dimensions by creating an addressable DNA box 42 × 36 × 36 nm3 in size that can be opened in the presence of externally supplied DNA ‘keys’. We thoroughly characterize the structure of this DNA box using cryogenic transmission electron microscopy, small-angle X-ray scattering and atomic force microscopy, and use fluorescence resonance energy transfer to optically monitor the opening of the lid. Controlled access to the interior compartment of this DNA nanocontainer could yield several interesting applications, for example as a logic sensor for multiple-sequence signals or for the controlled release of nanocargos.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Design of a DNA origami box.
Figure 2: AFM imaging of two- and three-dimensional DNA origami structures.
Figure 3: Characterization of DNA origami box by cryo-EM and small-angle X-ray scattering (SAXS).
Figure 4: Programmed opening of the box lid.

Similar content being viewed by others

Accession codes

Data deposits

The 3D map has been deposited in the EM Data Bank under the accession code EMD-1612.

References

  1. Seeman, N. C. An overview of structural DNA nanotechnology. Mol. Biotechnol. 37, 246–257 (2007)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  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)

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  5. 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  ADS  CAS  Google Scholar 

  6. Andersen, F. F. et al. Assembly and structural analysis of a covalently closed nano-scale DNA cage. Nucleic Acids Res. 36, 1113–1119 (2008)

    Article  CAS  Google Scholar 

  7. Yang, H. & Sleiman, H. F. Templated synthesis of highly stable, electroactive, and dynamic metal-DNA branched junctions. Angew. Chem. Int. Ed. 47, 2443–2446 (2008)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  10. Williams, B. A., Lund, K., Liu, Y., Yan, H. & Chaput, J. C. Self-assembled peptide nanoarrays: an approach to studying protein-protein interactions. Angew. Chem. Int. Ed. 46, 3051–3054 (2007)

    Article  CAS  Google Scholar 

  11. 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)

    Article  ADS  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  15. Simmel, F. C. Three-dimensional nanoconstruction with DNA. Angew. Chem. Int. Ed. 47, 5884–5887 (2008)

    Article  CAS  Google Scholar 

  16. 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 

  17. Ding, B. & Seeman, N. C. Operation of a DNA robot arm inserted into a 2D DNA crystalline substrate. Science 314, 1583–1585 (2006)

    Article  ADS  CAS  Google Scholar 

  18. Goodman, R. P. et al. Reconfigurable, braced, three-dimensional DNA nanostructures. Nature Nanotechnol. 3, 93–96 (2008)

    Article  ADS  CAS  Google Scholar 

  19. 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)

    Article  ADS  CAS  Google Scholar 

  20. Iqbal, A. et al. Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids. Proc. Natl Acad. Sci. USA 105, 11176–11181 (2008)

    Article  ADS  CAS  Google Scholar 

  21. Sander, B., Golas, M. M. & Stark, H. Advantages of CCD detectors for de novo three-dimensional structure determination in single-particle electron microscopy. J. Struct. Biol. 151, 92–105 (2005)

    Article  CAS  Google Scholar 

  22. van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17–24 (1996)

    Article  CAS  Google Scholar 

  23. Pedersen, J. S. A flux- and background-optimized version of the NanoSTAR small-angle X-ray scattering camera for solution scattering. J. Appl. Crystallogr. 37, 369–380 (2004)

    Article  CAS  Google Scholar 

  24. Svergun, D., Barberato, C. & Koch, M. H. J. CRYSOL - A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28, 768–773 (1995)

    Article  CAS  Google Scholar 

  25. Debye, P. Molecular-weight determination by light scattering. J. Phys. Colloid Chem. 51, 18–32 (1947)

    Article  CAS  Google Scholar 

  26. Sander, B., Golas, M. M. & Stark, H. Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra. J. Struct. Biol. 142, 392–401 (2003)

    Article  CAS  Google Scholar 

  27. Sander, B., Golas, M. M. & Stark, H. Corrim-based alignment for improved speed in single-particle image processing. J. Struct. Biol. 143, 219–228 (2003)

    Article  CAS  Google Scholar 

  28. Pedersen, J. S., Posselt, D. & Mortensen, K. Analytical treatment of the resolution function for small-angle scattering. J. Appl. Crystallogr. 23, 321–333 (1990)

    Article  Google Scholar 

  29. Pedersen, J. S. Analysis of small-angle scattering data from colloids and polymer solutions: modeling and least-squares fitting. Adv. Colloid Interface Sci. 70, 171–210 (1997)

    Article  CAS  Google Scholar 

  30. Clegg, R. M. et al. Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction. Methods Enzymol. 211, 353–388 (1992)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank R. Rosendahl Hansen and J. Kristensen for technical assistance. This work was supported by grants from the Danish National Research Foundation to the Centre for DNA Nanotechnology and the Danish Research Agency through support to the Interdisciplinary Nanoscience Center, by the Federal Ministry of Education and Research, Germany (0311899), and by the Sixth Framework Program of the European Union through the Integrated Project ‘3D Repertoire’ (H.S.).

Author information

Author notes

  1. Mingdong Dong

    Present address: Present address: Rowland Institute at Harvard, Harvard University, 100 Edwin H. Land Boulevard, Cambridge, Massachusetts 02142, USA.,

Authors and Affiliations

  1. Danish National Research Foundation: Centre for DNA Nanotechnology,,

    Ebbe S. Andersen, Mingdong Dong, Morten M. Nielsen, Kasper Jahn, Ramesh Subramani, Wael Mamdouh, Flemming Besenbacher, Kurt V. Gothelf & Jørgen Kjems

  2. Interdisciplinary Nanoscience Center,,

    Ebbe S. Andersen, Mingdong Dong, Morten M. Nielsen, Kasper Jahn, Ramesh Subramani, Wael Mamdouh, Cristiano L. P. Oliveira, Jan Skov Pedersen, Victoria Birkedal, Flemming Besenbacher, Kurt V. Gothelf & Jørgen Kjems

  3. Department of Molecular Biology,,

    Ebbe S. Andersen, Morten M. Nielsen, Kasper Jahn & Jørgen Kjems

  4. Department of Physics and Astronomy,,

    Mingdong Dong, Ramesh Subramani, Wael Mamdouh & Flemming Besenbacher

  5. The Water and Salt Research Center, Institute of Anatomy,,

    Monika M. Golas

  6. Stereology and EM Research Laboratory,,

    Bjoern Sander

  7. Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark,

    Cristiano L. P. Oliveira, Jan Skov Pedersen & Kurt V. Gothelf

  8. Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany ,

    Monika M. Golas, Bjoern Sander & Holger Stark

  9. Göttingen Centre for Molecular Biology, Justus-von-Liebig-Weg 11, University of Göttingen, D-37077 Göttingen, Germany

    Holger Stark

Authors
  1. Ebbe S. Andersen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mingdong Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Morten M. Nielsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kasper Jahn
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ramesh Subramani
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wael Mamdouh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Monika M. Golas
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bjoern Sander
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Holger Stark
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Cristiano L. P. Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Jan Skov Pedersen
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Victoria Birkedal
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Flemming Besenbacher
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Kurt V. Gothelf
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Jørgen Kjems
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Kurt V. Gothelf or Jørgen Kjems.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-9 with Legends and Supplementary Data. (PDF 1279 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Andersen, E., Dong, M., Nielsen, M. et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73–76 (2009). https://doi.org/10.1038/nature07971

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature07971

This article is cited by

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.

Search

Advanced 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