Materials World Network: Self-Assembled DNA Nanotubes: Biomimetic Design, Controlled Surface Alignment and Templated Nanowire Formation
Final Report Abstract
The synthesis of tubes is of general interest in nanotechnology. Due to their enhanced mechanical properties, nanotubes are well suited as templates for the build-up of functional hybrid structures. The main challenge is the development of reliable, self-assembly based synthesis routes which allow precise control over the geometrical parameters of the tubes. To this aim, we have developed different strategies for the self-assembly of nanotubes from deoxyribonucleic acid (DNA) following two generally different directions of assembly: tile-based structure formation and DNA origami. We have investigated the generically important case of tube assembly from a single-strand motif in detail. The high interest in this technique, first demonstrated by the group of Chengde Mao, arises from the application side. The synthesis of structures from a single-strand motif is the most costefficient way to build artificial DNA structures. We could demonstrate control over parameters such as diameter, length, chirality as well as branching, and in turn, over mechanical properties of artificial DNA tubes. Based on our experimental findings, we are able to derive models for the tube formation. Based on the models, we have performed experiments which clearly demonstrate how the applied design rules determine the diameter of the synthesized tubes. We were able to give new experimental insight into the formation mechanism of the single-stranded tubes reported by the Chengde Mao group. Tubular and cross-like structures were designed and synthesized by using DNA origami technique. The dependence of their geometry on the assembly conditions and controlled assembly of larger structures from origami elements were studied. The formation of artificially designed DNA structures by combining tile-based structure formation and DNA origami has been demonstrated. In the details, we have investigated the mineralization of these structures by site-specific nanoparticle attachment and by direct metal deposition from aqueous solution. The formation of tree-dimensional, regular nanoparticle arrays was shown. Based on local flow control and/or dielectrophoresis, we have developed surface alignment methods to assemble DNA and DNA nanotubes into networks, thereby bridging the bottom-up self-assembly with top-down lithographic approaches together. Measurements of physical properties of DNA have been performed. In particular, the electronic structure of DNA and the dependence of the geometrical and mechanical properties on intercalation of fluorescent dyes were investigated by spectroscopic methods and magnetic tweezers experiments, respectively.
Publications
- Controlling structural properties of self-assembled oligonucleotide-mercaptohexanol monolayers. Journal of Electron Spectroscopy and Related Phenomena, 2009, 172, 36-41
A. Kick, M. Bönsch, K. Kummer, D. V. Vyalikh, S. L. Molodtsov, M. Mertig
- Incorporation of DNA networks into microelectrode structures. Journal of Vacuum Science & Technology B, 2009, 27, 939-943
C. Erler, M. Mertig
- Photo-induced synthesis of DNA-templated metallic nanowires and their integration into microfabricated contact arrays. Applied Surface Science, 2009, 255, 9647-9651
C. Erler, K. Günther, M. Mertig
- Electronic structure of genomic DNA: A combined photoemission and X-ray absorption study. Journal of Physical Chemistry B, 2010, 114, 9645-9652
K. Kummer, D.V. Vyalikh, G. Gavrila, A.B. Preobrajenski, A. Kick, M. Bönsch, M. Mertig, S. L. Molodtsov
- Mechanical and structural properties of YOYO-1 complexed DNA. Nucleic Acid Research, 2010, 38, 6526-6532
K. Günther, M. Mertig, R. Seidel
- Self-assembly of DNA nanotubes with controllable diameters. Nature Communications, 2011, 2, 540
O.I. Wilner, R. Orbach, A. Henning, C. Teller, O. Yehezkeli, M. Mertig, D. Harries, I. Willner
- EGNAS: An exhaustive DNA sequence design algorithm. BMC Bioinformatics, 2012, 13, 138
A. Kick, M. Bönsch, M. Mertig
(See online at https://doi.org/10.1186/1471-2105-13-138) - Nanopatterning and Self-Assembly in Microsystems - an Overview. In: Gerald Gerlach, Klaus-Jürgen Wolter (Eds.): Bio and Nano Packaging Techniques for Electron Devices, Heidelberg, Berlin: Springer-Verlag, 2012, 179-208
W.-J. Fischer, M. Mertig
- Bio-Nanomaterials: Designing materials inspired by nature. Textbook, Wiley-VCH, 2013
W. Pompe, G. Rödel, H.-J. Weiss, M. Mertig
