Raphaël Barbey
The development of innovative bioanalytical technologies that enable the discovery of new therapeutics or the creation of systems for rapid, accurate and parallel analyses has gained an extraordinary interest in the biomedical sector in the last 10-15 years. Since proteins are the key-targets for such essential discoveries and developments, a particular emphasis has been placed on proteomics (study of proteins), including the investigation of protein structures, changes of protein expression upon treatment of cellular systems, the role of post-translational protein modifications on cell signaling events and the validation of selected proteins as disease-specific markers or pharmaceutical targets. These studies usually aim at using crude biological samples as the starting materials, which typically contain a large variety of proteins at concentrations covering a wide dynamic range and where the low abundant proteins are often the biologically most relevant. Therefore, the challenge is to create analytical tools which are able to cope with this large protein concentration range and which provide sufficiently high sensitivity to measure low abundant analytes in the presence of a high abundant protein matrix. The information that is expected from such technologies may soon exert a drastic change on the pace of medical research and considerably impact on the care of patients. As protein microarrays offer a powerful tool for the rapid, parallel analysis of complex samples and only require a minimal amount of reagents, they are currently one of the hot topics of life sciences, which strive to provide such analytical solutions. One of the current limiting factors in the field of protein microarrays for achieving the required analytical sensitivity is the amount of proteins that can be immobilized on the proteomic chip surface. Polymer brushes, which consist of an arrangement of polymer chains that are attached by one end to a substrate in a stretched, well-defined chain conformation, can increase the surface area available for protein binding, and thus act as a new category of 3D protein microarray substrates. With the advent of surface-initiated controlled polymerization techniques, extremely precise control over the thickness, composition, architecture and grafting density can be achieved, which allow to finely tune the properties of the polymer brush. In addition, these polymer chains may contain, natively or after specific post-polymerization reaction of their side chains, a high density of functional groups that can react with proteins. The different approaches available for the preparation of such surface-tethered polymer chains, the strategies allowing control over their architecture and properties as well as examples of applications related to protein binding are presented in Chapter 1. This Thesis describes the use of polymer brushes to create a new type of 3D proteomic chips, with the ultimate goal to improve the protein binding capacity compared to existing chip surface, without altering the accessibility of the detection reagents or increasing the intrinsic fluorescence of the background. The objective of this research work is to prepare polymer brush-based substrates that can outperform the sensitivity (i.e. increase the signal-to-noise ratio) that is obtained with a commercial microarray system, which is used as a benchmark in this Thesis. In this regard, functional polymer brushes containing epoxide groups that can react with the nucleophilic moieties of proteins have been chosen as promising candidates. In a preliminary set of experiments, the potential of glycidyl methacrylate-containing brushes to bind (bio)molecules via a post-polymerization modification reaction under mild conditions, i.e. at room temperature in aqueous medium, has been studied (Chapter 2). To this end, poly(glycidyl methacrylate) brushes, as well as several poly(glycidyl methacrylate)-co-poly(2-(diethylamino)ethyl methacrylate) copolymer brushes of different composition have been prepared by surface-initiated atom transfer radical (co)polymerization. The kinetics of the post-polymerization modification reaction of these (co)polymer brushes were followed using various model primary amines, as well as proteins. The introduction of tertiary amine groups, incorporated in the polymer brushes such as 2-(diethylamino)ethyl methacrylate units, was demonstrated not only to enhance the rate of the epoxide ring-opening reaction but also to induce higher protein binding capacities as compared to poly(glycidyl methacrylate) homopolymer brushes. The improved loading capacities of the (co)polymer brushes were evaluated in Chapter 3 under conditions that more closely resemble real microarray applications, such as the use of automated nanospotters to deposit proteins and fluorescence readers to detect protein immobilization. In this regard, commercially-available proteomic chips were coated with the epoxide-containing (co)polymer brushes and the spotting conditions as well as the proteins were varied. These studies revealed that the loading capacity depends on the pH and on the investigated protein, but also that the (co)polymer brush-coated substrates show far higher loading capacities than the standard, unmodified proteomic chips. This investigation also ascertained the supremacy of brushes containing 2-(diethylamino)ethyl methacrylate units compared to homopolymer brushes, as well as the superiority of thick (co)polymer brushes in comparison to their thinner equivalents. These (co)polymer brushes were subsequently used as platforms for real, although simplified, protein assays. The modified proteomic chips were spotted with unlabeled proteins that were further recognized with detection antibodies via either a one-step or a two-step approach. The clear benefits observed for copolymer brushes as compared to the existing technology under these realistic assay conditions nicely support the fact that the interior volume of the brush remains accessible for the detection reagents. In conclusion, the combination of the high loading capacity and the remaining accessibility for the detection partners make these (co)polymer brushes, and particularly the poly(glycidyl methacrylate)-co-poly(2-(diethylamino)ethyl methacrylate) brushes, excellent candidates for the improvement of the sensitivity in protein microarray applications.
EPFL2010
