Highlights 2008

About the centre

The Centre for DNA Nanotechnology (CDNA) was established on March 1, 2007 by Kjems, Besenbacher and Gothelf at Aarhus University 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. Among all the results obtained in 2008 the highlight was the formation of a DNA box as described in the following.

DNA Origami

The DNA origami method was introduced in 2006 [1] and has been ground breaking for the field of DNA nanotechnology. DNA origami is a design principle that allows efficient self-assembly of DNA into arbitrary shapes and patterns. An additional feature is that the structures formed are uniquely addressable which makes it possible to use it as a scaffold to position multiple nanobuilding blocks at fixed positions with high specificity. The DNA origami technique has provided a new tool to control matter at the nanoscale with applications for physics, chemistry and molecular biology and has thus been a major cohecive force in the CDNA center.

Development of DNA designer software

At the CDNA center we have taken on the challenge of developing dedicated DNA origami design software, which has been an essential step for making novel designs and investigating novel properties of DNA origami structures [2]. To advance the field of DNA nanotechnology and encourage the scientific community to contribute to the software development we have made the software freely available and open source, www.cdna.dk/origami/.

DNA Software

Constructing a box of DNA

A major challenge has been to extend the DNA origami technique into 3D, which was accomplished by coupling the 2D editor with a 3D viewer to create higher-order architectures. A DNA origami box of 42 x 36 x 36 nm3 was constructed using the software [3].  The six faces of the box were linked together by designing 3D-defining DNA stands. Two faces were designed as lids and an opening-closing mechanism was added.

Biophysical characterization

Self-assembly of 3D structures is a complex process that requires the correct positioning of larger elements (the faces of the box). That the designed box shape assembled correctly was verified by several complementary biophysical techniques. AFM allowed the study of controlled folding in 3D, cryo EM allowed the 3D reconstruction from single particles, and SAXS allowed studying the structure directly in solution [3]. Together these data showed that the DNA box assembles with high efficiency into well-defined box-shaped structures, with a size that is large enough to principally host a ribosome or a poliovirus.

DNA box - biophysical characterization

Programmed opening of the box lid

By using a FRET monitoring system it was shown that we can control the access to the interior of the DNA box depending on several "key" signals. Such a system has applications in controlling enzymatic activity by substrate access or as a complex biosensor coupled to release of nanocargo. The results have been accepted for publication in Nature.

DNA box model

References

[1]    Rothemund P. W. Folding DNA to create nanoscale shapes and patterns. Nature (2006) 440:297-302.

[2]    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) 2:1213-1218.

[3]    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.