Highlights 2010

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 CDNA as a programmable tool for directing the assembly of molecules and materials into nanoarchitectures and functional structures. The highlights for CDNA in 2010 are described in the following.

A novel dynamic DNA device with 11 controllable states

The dynamic nature of DNA hybridization has been utilized to design nanostructures that can switch between two or three geometrically well-defines states. We have created a new design that extends the controlled movement of a DNA structure to 11 discrete states (Figure 1).

Eleven discrete states

Figure 1 The DNA tile actuator locked in stages 0, 5 and 10; FRET interactions between the two fluorophores are used to characterize the motion of the actuator.

The actuator structure combines the fundamental motive of DNA nanotechnology, the double cross-over tile, with the mobile 4-way junction, known from Nature as the Holliday junction. The actuator has the ability to fine-tune the distances between attached components (resolution of less than 1 nm) for both physical studies of FRET interactions and control of chemical reactions. This work recently appeared in Angewandte Chemie where it was selected as a .“hot paper.”1

Inhibition of blood clogging using a new DNA nanostructure

CDNA associate Thom LaBean has in collaboration with two Danish PhD students designed a new DNA structure .– the weave tile, which is characterized by containing only 2 DNA strands.2 By extending the two sequences with two different thrombin-binding aptamers the weave tile can be used to increase the anticoagulant activity. Extended studies have shown that by the right choice of weave tile design a strong synergy between the two aptamers is observed. Furthermore, the binding to thrombin can be reversed.

Applications of DNA origami

In 2010 CDNA has continued exploring the DNA origami structure as a template for site-specific immobilization of materials and also for dynamic processes and we have published several articles in this area in 2010. In one example we have combined the action of light with AFM and DNA nanostructures to study the production of singlet oxygen from a single photosensitizer molecule on an origami structure.3We have demonstrated a distance-dependent oxidation of organic moieties incorporated in specific positions on DNA origami by singlet oxygen produced from a single photosensitizer located at the center of each origami (Figure 2).

AFM

Figure 2 DNA origami structure with a centrally positioned singlet oxygen sensitizer (green). The other 5 extended staple strands are modified with biotin (blue triangle). A 1O2 cleavable (SOC) linker molecule (red) is incorporated into the four staple strands positioned.

Single molecule imaging of guanine–potasssium interactions

In collaboration with Wei Xu, a former CDNA researcher, now Professor at Tongji University, China, we have studied the well-known guanine/potassium biological coordination system.4 In this study bioligand alkali metal coordination has for the first time been brought onto an inert Au(111) surface. Using the interplay between high-resolution scanning tunneling microscopy and density functional theory calculations, we show that the mobile G molecules on Au(111) can effectively coordinate with the K atoms, resulting in a metallosupramolecular porous network that is stabilized by a delicate balance between hydrogen bonding and metal-organic coordination, (Figure 3).

STM

Figure 3 UHV-STM guanine-potassium structures assembled on a Au(111) surface.

References

[1] A DNA Tile Actuator with 11 Discrete States.
Zhang, Z.; Olsen, E. M.; Kryger, M.; Voigt, N. V.; Tørring, T.; Gültekin, E.; Nielsen, M.; Zadegan, R. M.; Andersen, E.; Nielsen, M. M.; Kjems, J.; Birkedal, V.; Gothelf, K. V. Angew. Chem. Int. Ed. (2011), in press.

[2] Weave Tile Architecture: A Novel Construction Strategy for DNA Nanotechnology
Hansen, M.; Zhang, A.; Rangnekar, A.; Bompiani, K.; Carter, J.; Gothelf, K. V.; Labean, T. J. Am. Chem. Soc. (2010), 132, 14481–14486.

[3] Single Molecule Atomic Force Microscopy  Studies of Photosensitized Singlet Oxygen Behavior on a DNA Origami Template.
Helmig, S.; Rotaru, A.; Arian, D.; Arnbjerg, J.; Ogilby, P. R.; Kjems, J.; Mokhir, A.; Besenbacher, F.; Gothelf, K. V. ACS Nano (2010), 4, 7475–7480.

[4] Guanine and potassium based two-dimensional coordination network self-assembled on Au(111).
Xu, W.; Wang, J.; Yu, M.; Lægsgaard, E.; Stensgaard, I.; Linderoth, T.R.; Hammer, B.; Wang, C.; Besenbacher, F, J. Am. Chem. Soc. (2010) 132, 15927–15929.