Self-assembly is an attractive route towards construction at the nanoscale and is inspired by Nature where biomolecules readily self-assemble into well-defined and functional structures. In a “biokleptic” approach DNA nanotechnology has adapted naturally occurring structural DNA motifs to engineer geometrical shapes that can be efficiently self-assembled [1]. Recently, the DNA origami method was developed to build large two-dimensional DNA structures of arbitrary shape that can be used as a platform for arranging nanomaterials with high precision and specificity [2]. We have developed a software package for facilitating the design of DNA origami structures and initially used it to design the dolphins from the former logo of Aarhus University [3]. The software was further applied in the design of a three-dimensional DNA box with dimensions of 42 × 36 × 36 nm3 that can be opened and closed by external “key” signals [4]. The structure of the hollow DNA box is characterized by three structural techniques, cryogenic transmission electron microscopy, small-angle x-ray scattering, and atomic force microscopy, and opening of the lid was monitored optically by fluorescence resonance energy transfer. 

[1] Seeman, N. "Structural DNA nanotechnology: an overview". Methods Mol Biol 2005, 303, 143-66.

[2] Rothemund, P. W. "Folding DNA to create nanoscale shapes and patterns". Nature 2006, 440, 297-302.

[3] Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Lind-Thomsen, A., Mamdouh, W., Gothelf, K.V., Besenbacher, F., Kjems, J. "DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails". ACS Nano 2008, 2, 6, 1213-1218.

[4] Andersen, E. S., Dong, M., Nielsen, M. M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M. M., Sander, B., Stark, H.,  Oliveira, C. L. P.,  Pedersen, J. S., Birkedal, V., Besenbacher, F., Gothelf, K. V., Kjems, J. "Self-assembly of a nanoscale DNA box with a controllable lid". Nature 2009, in press.

Peter Staanum and Nicolai Nygaard