Highlights 2012

About the center

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. In 2012 the centre was extended to 2017.
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 2012 are described in the following.

 

Small DNA BOX with a reversible lid

The DNA origami box reported by CDNA in 2009 received considerable attention, not least due to the potential of the structure as a carrier of drugs, proteins or other materials. However, several technical improvements were required if the potential of the box should be realized. Two of these challenges were solved in a recent report by CDNA in ACS Nano.[1] In this study the BOX was shrinked to 18✕18✕24 nm3. The smaller size makes the box significantly more stable compared to the original structure and in addition, it was equipped with a new lid mechanism that allowed reversible closing and opening of the lid. In the new design the small BOX could potentially be used for a broad range of applications such as controlling the function of single molecules, controlled drug delivery, and molecular computing.

 Model of the small box with a lid that can be opened and closed continuously.

Figure 1. Model of the small box with a lid that can be opened and closed continuously.

 

Application of DNA origami to study DNA radiation Damage

Scanning probe microscopy methods play an important role in imaging DNA nanostructures and at CDNA we continue to develop the instrumentational methods for this purpose. Recently, a new atomic force microscopy (AFM) setup with sample temperature control was installed and it has enabled the study of thermally induced dynamics of DNA origami structures.[2]

In another study DNA origami was used as a platform to study low-energy electron (LEE) irradiation induced DNA damage.[3] We employed atomic force microscopy to image and quantify LEE-induced bond dissociations within specifically designed oligonucleotide (Figure 2). This novel technique allowed fast and parallel determination of DNA strand break yields with unprecedented control over the DNA's primary and secondary structure.

 

 Application of DNA origami to study sequence dependent low-energy electron (LEE) irradiation induced DNA damage at the single molecule level.

Figure 2. Application of DNA origami to study sequence dependent low-energy electron (LEE) irradiation induced DNA damage at the single molecule level.

Revealing electron transfer pathways in DNA helices

In an electrochemical study Feropontova et al. have studied the mechanisms of electron transfer reactions proceeding in dsDNA tethered to a gold electrode through an alkanethiol linker (Figure 3). DNAs were labeled with electrochemically active probes possessing redox potentials low enough to provide a “vertical” orientation of dsDNA on the negatively charged electrode surface. Two types of linkers, a short, conductive acetylene linker and a longer, less conductive alkane linker, and two types of redox probes, uncharged and positively charged, have been studied. Pertinent insight in the relation between electron transfer mechanism and the tethering of the redox probe was revealed in this paper that was published in J. Am. Chem. Soc. in 2012.[4] Among other things it was revealed that only if the redox probe is intercalated in the DNA helix, the electron transfer proceeds through the DNA helix.

 

 Electron transfer from an electrode surface to electroactive probes tethered to DNA in different ways.

Figure 3. Electron transfer from an electrode surface to electroactive probes tethered to DNA in different ways. 

DNA18 and dnatec conferences in Aarhus

On August 14-17, 2012, CDNA hosted the 18th International Conference on DNA Computing and Molecular Programming in Aarhus, August 14-17, 2012 in conjunction with a dnatec day on Monday, August 13. The DNA18 conference is one of two annual conferences that are organized by the International Society for Nanoscale Science Computing and Engineering (ISNSCE) and 170 participants attended the conferences (Figure 4).

 

Participants at the dnatec/DNA18 conference in Aarhus in August 2012 

Figure 4. Participants at the dnatec/DNA18 conference in Aarhus in August 2012

References


[1] Zadegan, R. M., Jepsen, M. D., Thomsen, K. E., Okholm, A. H., Schaffert, D. H., Andersen, E. S., Birkedal, V., Kjems, J. Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami. ACS Nano 2012, 6, 10050-10053.

[2] Song, J., Arbona, J., Zhang, Z., Liu, L., Xie, E., Elezgaray, J., Aime, J., Gothelf, K.V., Besenbacher, F. Dong, M. Direct Visualization of Transient Thermal Response of a DNA Origami. J. Am. Chem. Soc. 2012, 134, 9844-9847.

[3] Keller, A., Bald, I., Rotaru, A., Cauët, E., Gothelf, K. V., Besenbacher, F. Probing Electron-Induced Bond Cleavage at the Single-Molecule Level Using DNA Origami Templates. ACS Nano 2012, 6, 4392-4399.

[4] Abi, A., Ferapontova, E. E. Unmediated by DNA electron transfer in redox-labeled DNA duplexes end-tethered to gold electrodes. J. Am. Chem. Soc. 2012, 134, 14499–14507.