DNA Nanodevices

The work undertaken in this unit focuses on developing diagnostic and therapeutic applications of nanomaterials constructed by methods such as DNA self-assembly and molecular programming. Founded in 2013 as a part of the Fraunhofer Attract program, the unit’s aim is to develop concrete DNA-based tools for research and biomedicine, as well as to investigate and exploit the underlying material properties of nanoparticles built from DNA and composites. One aspect centers on the ability of DNA-based templates to serve as precise guides for the nanometer-scale arrangement of basic components for biosensors and nanocircuitry. Additionally, the unit develops functional platforms from DNA and other materials for the efficient transport of molecules in vitro and in vivo. Mechanical properties of DNA platforms as well as emergent properties from composites are also examined as possible instruments to increase the functional nature of hybrid materials.

DNA self-assembly and molecular programming

Currently, the most advanced method for the programmed assembly of nanometer-sized objects with well-controlled shapes and surface features uses DNA hybridization. Techniques like the DNA origami method or DNA “bricks” use the simple rules of complementary base pairing and placement of branched “Holliday” junctions between three or more DNA strands to generate complex two- and three-dimensional shapes. This enables DNA to serve as a highly programmable structural building block while stepping outside of the role of being the blueprint for cellular structure. Computer-assisted tools such as caDNAno and newly developed techniques for lab desk automation facilitate the rapid and precise creation of objects of virtually any shape on the nanometer scale.

Atomic Force Microscopy

Atomic Force Microscopy (AFM) is a tool for gaining precise structural and mechanical information about materials on a molecular scale. By scanning materials with a sharp tip just a few atoms in width, structural features can be resolved down to nanometer resolution. Furthermore, AFM-based force spectroscopy also allows the measurement of forces down to single piconewtons, and the local elastic properties of biological materials such as gels, cells and many more.

  • Development of molecular carrier and immunological systems from DNA and hybrid materials
  • Energy conversion and ordering phenomena in DNA-based and composite nanomaterials
  • Mechanical characterization of DNA-based and composite nanomaterials

  • University of Cologne, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institute for Biochemistry
  • pluriSelect GmbH
  • University of Leipzig, Faculty of Veterinary Medicine, Institute for Veterinary Anatomy
  • Chemnitz University of Technology, Department of Electrical Engineering and Information Technology, Center for Microtechnologies
  • LMU Munich, Faculty of Physics, Chair for Experimental Physics: Soft Condensed Matter
  • Yale University, Yale School of Medicine, Department of Molecular Biophysics and Biochemistry
  • TU Dresden, Biotechnology Center

  • Sajfutdinow M, Jacobs WM, Reinhardt A, Schneider C, Smith DM. Direct observation and rational design of nucleation behavior in addressable self-assembly. Proceedings of the National Academy of Sciences, 2018. 115(26): p. E5877-5886. doi.org/10.1073/pnas.1806010115 (open access)
  • Engel MC, Smith DM, Jobst MA, Sajfutdinow M, Liedl T, Romano F, Rovigatti L, Louis AA, Doye JPK. Force-Induced Unravelling of DNA Origami. ACS Nano, 2018. 12(7): p. 6374-6747. doi.org/10.1021/acsnano.8b01844 (no free version available)
  • Lorenz JS, Schnauß J, Glaser M, Sajfutdinow M, Schuldt C, Käs JA, Smith DM. Synthetic Transient Crosslinks Program the Mechanics of Soft, Biopolymer‐Based Materials. Advanced Materials, 2018. 30(13): p. 1706092. doi.org/10.1002/adma.201706092. (free preprint version)
  • Oswald L, Grosser S, Smith DM, Käs JA. Jamming transitions in cancer. Journal of Physics D Applied Physics, 2017. 50(48): p. 483001. doi.org/10.1088/1361-6463/aa8e83 (open access)
  • Schnauß J, Glaser M, Lorenz JS, Schuldt C, Möser C, Sajfutdinow M, Haendler T, Käs JA, Smith DM. DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers. Journal of Visualized Experiments: JoVE, 2017. 128. doi.org/10.3791/56056 (no free version available)
  • Schnauß J, Käs JA, Smith DM. Contact-free Mechanical Manipulation of Biological Materials. in Springer Handbook of Nanotechnology, 2017 Springer Press. p. 617-641. doi.org/10.1007/978-3-662-54357-3_20 (no free version available)
  • Sajfutdinow M, Uhlig K, Prager A, Schneider C, Abel B, Smith DM. Nanoscale patterning of self-assembled monolayer (SAM)-functionalised substrates with single molecule contact printing. Nanoscale, 2017. 9(39): p. 15098-15106. doi.org/10.1039/C7NR03696E (open access)
  • Schuldt C, Schnauß J, Händler T, Glaser M, Lorenz J, Golde T, Käs JA, Smith DM. Tuning Synthetic Semiflexible Networks by Bending Stiffness. Physical Review Letters, 2016. 117(9): p. 197801. doi.org/10.1103/PhysRevLett.117.197801 (free preprint version)
  • Glaser M, Schnauß J, Tschirner T, Schmidt BUS, Moebius-Winkler M, Käs JA, Smith DM. Self-assembly of hierarchically ordered structures in DNA nanotube systems. New Journal of Physics. 2016. 18(5): p. 055001. doi.org/10.1088/1367-2630/18/5/055001 (open access)
  • Nickels PC, Ke Y, Jungmann R, Smith DM, Leichsenring M, Shih WM, Liedl T, Högberg B. DNA origami structures directly assembled from intact bacteriophages. Small. 2014 May 14;10(9):1765-9. doi.org/10.1002/smll.201303442 (no free version available)
  • Schreiber R, Luong N, Fan Z, Kuzyk A, Nickels PC, Zhang T, Smith DM, Yurke B, Kuang W, Govorov AO, Liedl T. Chiral plasmonic DNA nanostructures with switchable circular dichroism. Nature Commuications, 2013. 4: p. 2948. doi.org/10.1038/ncomms3948 (open access)
  • Smith DM, Schüller V, Engst C, Rädler J, Liedl T. Nucleic acid nanostructures for biomedical applications. Nanomedicine, 2013. 8(1): p. 105-121. doi.org/10.2217/nnm.12.184 (no free version available)
  • Smith DM, Schüller V, Forthmann C, Schreiber R, Tinnefeld P, Liedl T. A structurally variable hinged tetrahedron framework from DNA origami. J. Nuc. Acid., 2011. dx.doi.org/10.4061/2011/360954 (open access)