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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.

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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.

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Data deposits

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

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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

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  1. Ebbe S. Andersen
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Correspondence to Kurt V. Gothelf or Jørgen Kjems.

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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

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