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Nature 459, 73-76 (7 May 2009) | doi:10.1038/nature07971; Received 9 November 2008; Accepted 6 March 2009

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

Ebbe S. Andersen1,2,3, Mingdong Dong1,2,4,10, Morten M. Nielsen1,2,3, Kasper Jahn1,2,3, Ramesh Subramani1,2,4, Wael Mamdouh1,2,4, Monika M. Golas5,8, Bjoern Sander6,8, Holger Stark8,9, Cristiano L. P. Oliveira2,7, Jan Skov Pedersen2,7, Victoria Birkedal2, Flemming Besenbacher1,2,4, Kurt V. Gothelf1,2,7 & Jørgen Kjems1,2,3

  1. Danish National Research Foundation: Centre for DNA Nanotechnology,
  2. Interdisciplinary Nanoscience Center,
  3. Department of Molecular Biology,
  4. Department of Physics and Astronomy,
  5. The Water and Salt Research Center, Institute of Anatomy,
  6. Stereology and EM Research Laboratory,
  7. Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
  8. Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
  9. Göttingen Centre for Molecular Biology, Justus-von-Liebig-Weg 11, University of Göttingen, D-37077 Göttingen, Germany
  10. Present address: Rowland Institute at Harvard, Harvard University, 100 Edwin H. Land Boulevard, Cambridge, Massachusetts 02142, USA.

Correspondence to: Kurt V. Gothelf1,2,7Jørgen Kjems1,2,3 Correspondence and requests for materials should be addressed to K.V.G. (Email: kvg@chem.au.dk) or J.K. (Email: jk@mb.au.dk).

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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 times 36 times 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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