Highlights 2009

About the centre

Centre for DNA Nanotechnology (CDNA) was established in March 2007 by Kjems, Besenbacher and Gothelf in collaboration with the two American researchers Yan and LaBean. The purpose of the research at CDNA is to explore fundamental aspects of DNA as a programmable tool for directing the assembly of molecules and materials into nanoarchitectures and functional structures. The highlights for CDNA in 2009 are described in the following.

Publication of CDNA research in Nature

The design and characterization of a DNA origami box was described as the highlight of the former year. This work was, however, not published until May 2009 in the international leading scientific journal Nature [1]. The publication and the overwhelming international attention has been one of the main highlights of 2009. After the publication, the article was commented in several international media, e.g. National Geographics and The Wall Street Journal as shown below in Figure 1. By the end of 2009 the Danish engineering magazine Ingeniøren selected the DNA box as the most important research in Denmark in 2009.

Image from Wall Street Journal

Single molecule chemical reactions on DNA origami

DNA origami – the folding of a long natural DNA sequence using around 200 synthetic DNA sequences – has continued to be one of the main areas for the research at CDNA in 2009. As one of the highlights in 2009, we have shown that it is possible to perform chemical reactions of DNA origami and to form images of single molecule chemical reactions. To realize this we have used a 70 x 100 nm2 “carpet” of DNA origami, which is form by self-assembly. In the DNA carpet the individual positions of the approximately half a million of atoms that constitute the structure, are known with high precision. If reactive functional groups are built into the carpet, their exact position in the carpet will be known. When the DNA carpets are immobilized on a surface it becomes possible to follow the chemical reactions that take place on the surface by atomic force microscopy (AFM). Normally, small molecules cannot be imaged by AFM and larger molecules such as proteins will appear as dots that cannot be distinguished. The great advantage of the new method is that the exact position of the chemical reaction at the origami surface is known and thereby it is possible to identify and distinguish different chemical reactions. The principle is exemplified in Figure 2. In the top of the figure an origami structure is shown, containing three different reactive chemical groups and a biotin molecule (green) as the reference. Three different molecules (shown in the middle of the figure) will react with the complementary functional group at the surface, e.g. the activated ester will react with the amine. In this manner it can be predicted in which position it is suppose to react. The molecule that reacts at the surface also contains a biotin unit and subsequent binding of the large protein streptavidin to the biotins makes it possible to make images of the outcome of the chemical reactions on the DNA origami. The positions that have reacted (and the reference position) appear as bright dots on the origami surface. The reactions proceed in a high yield of around 90%.

DNA Origami by AFM

This work demonstrates a fundamentally new method to make images of reactions of single molecules, and it demonstrates for the fist time that it is possible to make covalent bonds on complex DNA nanostructures. It is a first step towards making advanced chemical synthesis on DNA platforms, where the selectivity in the chemical reactions is determined by the position at the surface rather than the functional groups in the molecule. The results were published in the leading nanotechnology journal Nature Nanotechnology in February 2010.

References

[1] 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 nano-scale DNA box with a controllable lid. Nature (2009), 459, 73-76.

[2] Voigt, N. V.; Tørring, T.; Rotaru, A.; Jacobsen, M. F.; Lauritzen, J. B.; Subramani, R.; Mamdouh, W.; Kjems, J.; Mokhir, A.; Besenbacher, F.; Gothelf, K. V. Single Molecule Chemical Reactions On DNA Origami. Nature Nanotech. (2010), 5, 200.