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Dr Stefan Howorka

Research Overview

Our group studies and engineers the self-assembly of bio-polymers into nano-architectures of emergent functional properties.

Membrane nanopores from self-assembled DNA: Nucleic acids chemistry and single-molecule detection

Membrane-spanning nanopores are widespread in nature and facilitate the essential transport of water-soluble molecules across bilayers. Replicating this key property with engineered or de-novo pores is scientifically intriguing and additionally leads to powerful biomedical research tools and biosensor components. The Howorka group has created stable DNA-based nanopores that structurally mimic the amphiphilic nature of protein pores and insert into bilayers to support a steady transmembrane flow of ions [1]. As folded DNA is a versatile material for the bottom-up construction, the new DNA-nanopores are expected to open up the design of entirely new molecular devices for a broad range of applications including sensing, electric circuits, catalysis, and research into nanofluidics and controlled transmembrane transport. The generation of nanopores via DNA assembly also merges our group’s previously separate research interests in nanopores [2-4] and the chemical modification of nucleic acids [5-7].

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Self-assembled nanolattices: Structural investigations and protein engineering

Among natural protein assemblies, S-layers stand out as a major two-dimensional cell-wall component in archaea and many pathogenic and biotechnologically relevant bacteria. The nanoscale repeat structure of the self-assembled S-layer lattices has also sparked interest in their use as patterning and display scaffolds for several nanobiotechnological applications including vaccine carriers [8]. Initiated by our group’s examination of their molecular architecture with chemical and genetics tools [9, 10], the structure of a model S-layer has been elucidated to atomic resolution in collaboration with Prof. Han Remaut [11]. This unprecedented structural insight will help guide the rational engineering of the protein lattices for biomedicine and biophysics.

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Surface nanopatterns: Surface modification and ultrasensitive detection

Modifying solid substrates with self-assembled polymer films is an attractive strategy to tailor surface properties for applications in biosensing and biological research. Our group has worked on poly(ethylene glycol) (PEG) layers to understand their physico-chemistry and to hone the films’ functional performance in microarrays [12, 13]. The optimised surfaces feature improved specific and lower non-specific DNA binding and have thus enabled microarray read-out at the scientifically and diagnostically relevant single-molecule level [14]. More recently, the assembled polymer films were exploited to create protein nanopatterns for biophysics and cell biology. In particular, carbon-nanoislands were written with an electron-beam and fluorescence-labelled protein bound to the nanoislands but not to the surrounding PEG-coated surface [15]. The nanopatterning strategy helps to control the surface density of surface-bound biomolecules as playfully illustrated by creating a microscale version of Renaissance painting composed of nanoscale pixels of different brightness. Currently, nanopatterned surfaces are being used as research tools on cells that respond to the nanoscale densities of activating molecules.

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Selected Publications

  1. Burns, J.; Stulz, E.; Howorka, S. Nano Lett. 2013, published online Apr 30, nl304147f
  2. Howorka, S.; Siwy, Z. S. Nat Biotechnol 2012, 30, (6), 506-507.
  3. Howorka, S.; Siwy, Z. Chem. Soc. Rev. 2009, 38, (8), 2360-2384.
  4. Howorka, S.; Cheley, S.; Bayley, H. Nat. Biotechnol. 2001, 19, (7), 636-39.
  5. Mitchell, N.; Howorka, S. Angew. Chem. Int. Ed. 2008, 47, (30), 5476-5479.
  6. Mitchell, N.; Schlapak, R.; Kastner, M.; Armitage, D.; Chrzanowski, W.; Riener, J.; Hinterdorfer, P.; Ebner, A.; Howorka, S. Angew. Chem. Int. Ed. 2009, 48, (3), 525-527.
  7. Borsenberger, V.; Howorka, S. Nucleic Acids Res. 2009, 37, (5), 1477-1485.
  8. Howorka, S. Curr. Opin. Biotechnol. 2011, 22, (4), 485-491.
  9. Kinns, H.; Howorka, S. J. Mol. Biol. 2008, 377, (2), 589-604.
  10. Kinns, H.; Badelt-Lichtblau, H.; Egelseer, E. M.; Sleytr, U. B.; Howorka, S. J. Mol. Biol. 2010, 395, (4), 742-753
  11. Baranova, E.; Fronzes, R.; Garcia-Pino, A.; Van Gerven, N.; Papapostolou, D.; Péhau-Arnaudet, G.; Pardon, E.; Steyaert, J.; Howorka, S.; Remaut, H. Nature 2012, 487, 119-122.
  12. Schlapak, R.; Armitage, D.; Saucedo-Zeni, N.; Chrzanowski, W.; Hohage, M.; Caruana, D.; Howorka, S. Soft Matt. 2009, 5, (3), 613-621.
  13. Schlapak, R.; Pammer, P.; Armitage, D.; Zhu, R.; Hinterdorfer, P.; Vaupel, M.; Fruhwirth, T.; Howorka, S. Langmuir 2006, 22, (1), 277-285.
  14. Zhu, R.; Howorka, S.; Proll, J.; Kienberger, F.; Preiner, J.; Hesse, J.; Ebner, A.; Pastushenko, V. P.; Gruber, H. J.; Hinterdorfer, P. Nat. Nanotechnol. 2010, 5, (11), 788-791.
  15. Schlapak, R.; Danzberger, J.; Haselgrubler, T.; Hinterdorfer, P.; Schaffler, F.; Howorka, S. Nano Lett. 2012, 12, (4), 1983-1989.