Small-molecule nucleic acids chemistry

My group is developing new chemistries to create modified nucleosides and nucleotides that can be used to facilitate chemical biological research. A specific focus is the synthesis of light-sensitive nucleic acid derivatives carrying either fluorophores or light-removable photocages. In the first line of research, my group has developed a Diels-Alder chemistry for nucleotides to facilitate the efficient, mild, and orthogonal labelling of DNA strands with fluorophores [1]. The chemistry can also be applied for the labelling with large peptides [2]. Other examples include improved chemistries for the phosphorylation of nucleosides [3]. Within the second, more recent line of research, biomedically important nucleoside analogues are being synthesised with photoremovable groups to regulate their bioactivity within cells.

Howorka Diels Alder

Lipid-bilayer-anchored nucleic acids: Membrane nanopores from folded DNA

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 by equipping oligonucleotides with hydrophobic lipid anchors and folding them into membrane-spanning pores (Angewandte Chemie, front cover) [4,5]. As 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 single-molecule sensing, controlled transmembrane transport and drug delivery, and synthetic biology. The generation of nanopores from chemically modified DNA continues my previous research interests in protein nanopores [6-8].


Linker chemistry: Anchoring nucleic acids to solid surfaces

The immobilisation of DNA and other biomolecules to inorganic surfaces is important for bioanalysis schemes, chromatography, and the biofunctionalisation of nanoparticles. Chemical linkers that couple the molecular receptors to the surface are essential to maintain the specific recognition activity. My group has been successfully working with poly(ethylene glycol), alkane, and nucleic acids-based linkers [9-12] to achieve the oriented, high-density, and spatially defined immobilisation of DNA strands and molecular receptors. In microarrays, the organic surface layers improve the specific binding of DNA analytes while lowering the non-specific adsorption of non-target strands [10]. Based on their advantageous properties, the linker chemistries have been utilised for the ultrasensitive sensing of diagnostically important RNA species which remain undetected in conventional analytical schemes. As further highlight, epigenetically relevant methylated DNA strands could be analysed at the single-molecule level in collabortion with Prof. Hinterdorfer as published in Nature Nanotechnology  [13].

Structural investigations of self-assembled protein lattices

In previous research activities, the structure of bacterial exoskeleton protein was investigated to achieve a world-first as published in Nature [14]. The planar protein lattices, termed 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 [15]. Driven by my group's examination of the molecular architecture with chemical and genetics tools within a 10-year long quest [16-18], the structure of a model S-layer has been elucidated in 2012 to atomic resolution as a world-first in collaboration with Prof. Remaut [14]. The unprecedented structural insight can help guide the rational engineering of the protein lattices for biomedicine and biophysics.

Selected Publications

[1] V. Borsenberger, S. Howorka, Nucleic Acids Res. 2009, 37, 1477-1485.

[2] V. Borsenberger, N. Mitchell, S. Howorka, J. Am. Chem. Soc. 2009, 131, 7530-7531.

[3] V. Borsenberger, M. Kukwikila, S. Howorka, Org. Biomol. Chem. 2009, 7, 3826 - 3835.

[4] J. Burns, E. Stulz, S. Howorka, Nano Lett. 2013, 13, 2351-2356.

[5] J. R. Burns, K. Göpfrich, J. W. Wood, V. V. Thacker, E. Stulz, U. F. Keyser, S. Howorka, Angew. Chem. Int. Ed. 2013, 52, 12069–12072.

[6] S. Howorka, Z. S. Siwy, Nat. Biotechnol. 2012, 30, 506-507.

[7] S. Howorka, Z. Siwy, Chem. Soc. Rev. 2009, 38, 2360-2384.

[8] S. Howorka, S. Cheley, H. Bayley, Nat. Biotechnol. 2001, 19, 636-639.

[9] Schlapak, R., J. Danzberger, D. Armitage, D. Morgan, P. D. Pollheimer, H. J. Gruber, F. Schäffler, S. Howorka Small. 2012, 8, 89-97

[10] R. Schlapak, P. Pammer, D. Armitage, R. Zhu, P. Hinterdorfer, M. Vaupel, T. Fruhwirth, S. Howorka, Langmuir 2006, 22, 277-285.

[11] N. Mitchell, R. Schlapak, M. Kastner, D. Armitage, W. Chrzanowski, J. Riener, P. Hinterdorfer, A. Ebner, S. Howorka, Angew. Chem. Int. Ed. 2009, 48, 525-527.

[12] P. D. Pollheimer, M. Kastner, A. Ebner, D. Blaas, P. Hinterdorfer, H. J. Gruber, S. Howorka, Bioconjug. Chem. 2009, 20, 466–475.

[13] R. Zhu, S. Howorka, J. Proll, F. Kienberger, J. Preiner, J. Hesse, A. Ebner, V. P. Pastushenko, H. J. Gruber, P. Hinterdorfer, Nat. Nanotechnol. 2010, 5, 788-791.

[14] E. Baranova, R. Fronzes, A. Garcia-Pino, N. Van Gerven, D. Papapostolou, G. Péhau-Arnaudet, E. Pardon, J. Steyaert, S. Howorka, H. Remaut, Nature 2012, 487, 119-122.

[15] S. Howorka, Curr. Opin. Biotechnol. 2011, 22, 485-491.

[16] S. Howorka, M. Sára, Y. Wang, B. Kuen, U. B. Sleytr, W. Lubitz, H. Bayley, J. Biol. Chem. 2000, 275, 37876-37886.

[17] H. Kinns, S. Howorka, J. Mol. Biol. 2008, 377, 589-604.

[18] H. Kinns, H. Badelt-Lichtblau, E. M. Egelseer, U. B. Sleytr, S. Howorka, J. Mol. Biol. 2010, 395, 742-753