Fabrication of protein and ssDNA patterns in the protein-repelling matrix by electron beam and ultraviolet lithography

Michael Zharnikov

Applied Physical Chemistry, Heidelberg University, 69120 Heidelberg, Germany


Fabrication of well-defined protein patterns on solid substrates is important for cell culture research, proteomics, and biosensors. Frequently, such patterning involves the use of protein-repelling poly(ethylene glycol) (PEG) films or oligo(ethylene glycol) terminated alkanethiolate (OEG-AT) monolayers as a background, which is necessary to prevent the nonspecific adsorption of proteins beyond the preselected areas. Usually, the OEG-AT species are introduced by backfilling process, after patterning protein-binding molecules on the substrate. I present here an alternative, more simple and straightforward approach, viz. the writing of protein-affinity patterns directly in the protein-repelling OEG-AT or PEG matrix by electron beam or ultraviolet lithography (EBL and UVL, respectively). Utilizing the high sensitivity of the OEG and PEG backbones to electrons and UV light, they can be continuously damaged with progressive irradiation, resulting in a gradual and controlled change of the protein-repelling properties. Based on this behaviour, protein affinity patterns can be directly written in a protein-repelling matrix and serve as templates for the subsequent attachment of proteins. Employing this direct writing (DW) approach not only simple “black-white” but also comparably complex “gray-scale” (gradient-like) patterning of proteins was achieved. The only limitation is that the DW procedure relies basically on non-specific adsorption of proteins, which is not always desirable and, in some selected cases, can lead to denaturation of the proteins thereby affecting further their performance and activity. However, a non-specific, OEG-AT based template, generated by EBL or UVL, can be transformed to a specific one by employing irradiation-promoted exchange reaction (IPER). Within this approach, an irradiated OEG-AT monolayer is subjected to exchange reaction in the course of which the partly damaged OEG-AT moieties in the primary matrix are exchanged for potential molecular substituents bearing a special receptor group for specific binding of the target protein or ssDNA strand. The rate and extent of IPER depend on the density of irradiation-induced defects in the OEG-AT monolayer, which can be precisely controlled by the selection of a suitable dose within a certain dose range. Using the DW and IPER approaches in combination with EBL and UVL, we demonstrated the fabrication of complex non-specific, specific, and multiple protein patterns as well as ssDNA patterns and polymer brushes formed on the ssDNA/OEG-AT templates by surface-initiated enzymatic polymerization.

Summary of academic career

Michael Zharnikov has received a Master degree (with honor) in Solid State Physics from the Moscow Engineer-Physical Institute in 1981. From 1981 to 1991 he worked in Kurchatov Atomic Energy Institute in Moscow, where he received a PhD degree in Experimental Physics in 1989. In 1991 he moved to Germany. After 2 post-doctoral stints with Prof. Dietrich Menzel at the Technical University Munich (1991-1994) and Prof. Jürgen Kirschner at Max-Planck Institute für Mikrostrukturphysik in Halle/Saale (1994-1996), Zharnikov joined the Faculty of Chemistry and Geosciences at the Heidelberg University first as Senior Scientist (group of Prof. Michael Grunze) and later, after habilitation, as Privat-Dozent (2001) and Prof. apl. (2008). Zharnikov published 287 peer-reviewed journal articles and book chapters (H=46, ca. 8100 citations), obtained 2 patens, and delivered about 140 lectures, including 55 invited talks at national and international conferences. His group at Heidelberg University is actively involved in research related to the fabrication of functional organic surfaces, interfacial engineering, biointerfaces, molecular sensors, soft matter nanofabrication, e-beam and UV lithography, molecular and organic electronics, design of novel materials, molecular structure of liquids, and advanced X-ray spectroscopy. His activities involve a frequent use of synchrotron radiation facilities over the world, including BESSY II in Berlin, Max IV in Lund, and ALS in Berkeley. Zharnikov is a member of the Editorial Boards of J. Electron Spectrosc. Relat. Phenom. and J. Vac. Sci. Technol.