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.

Pinpointed stimulation of EphA2 receptors via DNA-templated oligovalence

Receptor clusters are formed by the peptide-coupled DNA trimers binding to EphA2 receptors (green). This leads to the autophosphorylation and activation of tumor-suppressing signaling pathways
© Fraunhofer IZI

Receptor clusters are formed by the peptide-coupled DNA trimers binding to EphA2 receptors (green). This leads to the autophosphorylation and activation of tumor-suppressing signaling pathways.

The field of DNA nanotechnology utilizes DNA strands not for their genetic encoding capabilities, but rather as construction materials. Using rational design principles, individual DNA strands can be assembled into precise nanostructures of nearly any shape. These nanostructures allow functional molecules such as peptides to be attached to nearly any unique location on their structure. Since structural features can be altered with the spatial resolution of a single base pair (0.34 nanometers), several molecules can be attached in closely controlled geometry. When these molecules are ligands that bind to specific targets, their spatial arrangement can be controlled according to the desired target’s geometry. This results in optimized binding and/or signaling interactions.

In this project, the efficacy of SWL, an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, was enhanced by a factor of nearly four orders of magnitude by presenting three of these peptides on small DNA nanostructures in an oligovalent manner. Ephrin signaling pathways are critical in the development and progression of many types of cancer, and are potential targets in cancer diagnosis, imaging and treatment.

Here, the impact of SWL valency on binding affinity, phosphorylation (a key player for activation) and the regulation of phenotype prostate cancer cells that express EphA2 was quantitatively demonstrated. DNA structures with three SWL peptides significantly enhanced EphA2 phosphorylation by 8000-fold. Furthermore, the pinpointed interaction of these constructs showed an enhanced impact on the retraction of cells compared to one of EphA2’s natural ligands – ephrin-A1. These results demonstrated that simple DNA structures can be used to greatly enhance the potency of otherwise weak signaling peptides, using principles of a nanometer-scale oligovalent arrangement.

Programming biomaterial mechanics with DNA

Examples of bundled, star-like, connected and compact microparticle structures formed from DNA tubes. (from New J. Phys. 18 (5), 055001)

Examples of bundled, star-like, connected and compact microparticle structures formed from DNA tubes. (from New J. Phys. 18 (5), 055001).

Beyond its standard role as the carrier of genetic information in living organisms, DNA has also emerged has highly versatile construction material for fabricating nanometer-sized particles and machines. By carefully designing the sequences of DNA strand collections, complementary base pairing can be used to fully control the size, shape and mechanical properties of single, DNA-based nanoparticles or larger DNA-based materials.

An example includes materials formed from DNA nanotubes. A small collection of DNA strands is designed to self-assemble into micrometer-length filaments. Their nanometer-sized diameters can be precisely controlled in order to "program" their nanoscale mechanical properties. These can act as synthetic mimics of biologically derived structures such as actin or collagen filaments. However, the programmable nature of DNA strands provides the ability to selectively control parameters such as the stiffness of the individual nanotubes, which is not possible with biologically derived materials such as actin or collagen.

By forming the DNA nanotubes in a crowded molecular environment, similar to what is found inside cells, they can be made to spontaneously assemble large microstructures that are dependent upon their stiffness and volume fraction (Figure 1). These star-like or bundled structures resemble cellular structures such as stress fibers, filopodia or the mitotic spindle, and are tools to provide insight into the basic mechanism behind their formation in biological systems.

Additionally, DNA nanotubes at lower volume fractions form entangled, elastic hydrogels. Here, the elastic plateau shear modulus (G') can be adjusted over a wide range by changing either the network density or the stiffness of the individual DNA nanotubes. This enables a fine-tuning of the hydrogel stiffness while being able to independently maintain factors such as porosity. This ability to control macroscale properties through programmable nanoscale building blocks can be applied more broadly to develop functional materials for cell-based applications such as 3D cell culture or nutrient repositories in long-term bioreactors.

Further projects

  • 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

  • Möser C, Lorenz JS, Sajfutdinow M, Smith DM. Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence. International Journal of Molecular Sciences (2018), Nr.19, 19 S. dx.doi.org/10.3390/ijms19113482
  • 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)