Control of protein immobilization at sensor surfaces is of great interest within various scientific fields, since it enables studies of specific biomolecular interactions. To achieve this, one must be able to immobilize proteins with retained native structure, while minimizing non-specific protein binding. The high affinity interaction between streptavidin (SA) and biotin is extensively used as a linker between a surface, where SA is immobilized, and the (biotinylated) molecule of interest. Self- assembled monolayers (SAMs) of poly- and oligo ethylene glycol (PEG and OEG) derivatives have been proven in literature to minimize non-specific protein binding, and biotin-exposing SAMs have been shown efficient for immobilization of SA. The aim of this master's thesis project was to develop biotinylated gold surfaces for quartz crystal microbalance with dissipation monitoring (QCM-D) applications through the self-assembly of mixed monolayers of thiolated OEG (or PEG) derivatives with or without a terminal biotin head group. For this, different thiol compounds were to be compared and evaluated. For the systems under study, the required biotin density for maximum specific SA immobilization was to be established, while keeping the non-specific serum adsorption at a minimum. Model experiments with biotinylated proteins immobilized to the SA-functionalized surfaces were to be performed to evaluate the possibilities for commercialization. A protocol for the preparation of a novel biotinylated surface was developed based on the immersion of gold substrates in an ethanolic incubation solution of dithiols with OEG chains (SS-OEG and SS-OEG-biotin, 99:1) and found to give reproducible results with respect to low non-specific protein binding and immobilization of a monolayer of SA. The modified surfaces allowed for subsequent immobilization of biotinylated bovine serum albumin (bBSA) and biotinylated plasminogen (bPLG). PLG was the subject of a challenging case study, using a combination of QCM-D and surface plasmon resonance (SPR), where the immobilized protein was subjected to low molecular weight ligands that were believed to induce conformational changes. The high control of the surface chemistry allowed for the interpretation of the increased dissipation shift upon ligand binding in terms of conformational changes. An obstacle before commercialization of the described biotinylated surfaces is that they do not seem stable for storage > 7 days. The reasons for this have to be investigated further.

Polymer/inorganic nanoparticle hybrid thin films, primarily composed of functional inorganic nanoparticles, are of great interest to researchers because of their interesting electronic, photonic, and optical properties. In the past two decades, layer-by-layer (LbL) assembly has become one of the most powerful techniques to fabricate such hybrid thin films. This method offers an easy, inexpensive, versatile, and robust fabrication technique for multilayer formation, with precisely controllable nanostructure and tunable properties. In this thesis, various ways to control the structure of hybrid thin films, primarily composed of polyelectrolytes and indium tin oxide (ITO), are the main topics of study. ITO is one of the most widely used conductive transparent oxides (TCOs) for applications such as flat panel displays, photovoltaic cells, and functional windows. In this work, polyethyleneimine (PEI) was used to stabilize the ITO suspensions and improve the film buildup rate during the LbL assembly of poly(sodium 4-styrenesulfonate) (PSS) and ITO. The growth rate was doubled due to the stronger interaction forces between the PSS and PEI-modified ITO layer. The assembly of hybrid films was often initiated by a polyelectrolyte precursor layer, and the characteristics of the precursor layer were found to significantly affect the assembly of the hybrid thin films. The LbL assembly of ITO nanoparticles was realized on several substrates, including cellulose fibers, write-on transparencies, silicon wafers, quartz crystals, and glasses. By coating the cellulose fibers with ITO nanoparticles, a new type of conductive paper was manufactured. By LbL assembly of ITO on write-on transparencies, transparent conductive thin films with conductivity of 10⁻⁴ S/cm and transparency of over 80 % in the visible range were also prepared. As a result of this work on the mechanisms and applications of LbL grown films, the understanding of the LbL assembly of polyelectrolytes and inorganic nanoparticles was significantly extended. In addition to working with ITO nanoparticles, this thesis also demonstrated the ability to grow bicomponent [PEI/SiO₂]n thin films. It was further demonstrated that under the right pH conditions, these films can be grown exponentially (e-LbL), resulting in much thicker films, consisting of mostly the inorganic nanoparticles, in much fewer assembly steps than traditional linearly grown films (l-LbL). These results open the door to new research opportunities for achieving structured nanoparticle thin films, whose functionality depends primarily on the properties of the nanoparticles.

The investigations are related to the influence of nonionic polyethoxylated surfactant on Tin- and Tin-Silver depositions. Cyclovoltammetry, electrochemical depositions in Hull cell, with quartz crystal microbalance, impedance spectroscopy, X-ray diffraction, REM and others were used as methods of characterization. / Die Untersuchungen befasssen sich mit dem Einfluss von nichtionischen polyethoxylierten Tenside auf die Zinn- und Zinn-Silber-Abscheidung, die durch Zyklovoltammetrie, Abscheidungen in der Hullzelle, mit der elektrochemischen Quarzmikrowaage, der Impedanzspektroskopie, Röntgendiffraktometrie, Rasterelektronenmikroskopie und Tensiometrie charakterisiert wurden.

This thesis mainly deals with the development of photochemical approaches to immobilize carbohydrates on surfaces for glycobiological studies. These approaches have been incorporated into a number of state-of-the-art nanobio-platforms, including carbohydrate microarrays, surface plasmon resonance (SPR), quartz crystal microbalance (QCM), atomic force microscopy (AFM), and glyconanomaterials. All the surfaces have displayed good binding capabilities and selectivities after functionalization with carbohydrates, and a range of important data have been obtained concerning surface characteristics and carbohydrate-protein interactions, based on the platforms established. Besides, a variety of non-carbohydrate and carbohydrate-based molecules have been synthesized, during which process the mutarotation of 1-glycosyl thiols and the stereocontrol in 1-S-glycosylation reactions have been thoroughly studied. / QC 20111004

Les nanoparticules de silice sont des plateformes idéales pour la conception d’outils de bioimagerie afin d’étudier les mécanismes de transfert de gènes par des lipoplexes. L’objectif de notre étude est le développement d’une modification chimique de surface permettant d’obtenir des colloïdes de silice chargés positivement susceptible de lier de l’ADN par des interactions électrostatiques. Deux stratégies pour la génération de groupements ammonium quaternaires sur des nanoparticules de silice sont présentées a) une silanisation directe par l’utilisation d’un agent de couplage silanique contenant un groupement ammonium quaternaire et b) un procédé en deux étapes mettant en jeu une modification de surface chimique par des aminosilanes primaires et secondaires suivie d’une alkylation des amines par l’iodomethane. Différentes méthodes physico-chimiques (essais de cosédimentation, des expériences de microbalance à cristal de quartz avec mesure de dissipation et d’imagerie MET et Cryo-MET) ont été utilisées pour mettre en évidence et caractériser les interactions entre les biomolécules et les surfaces quaternisées. Des études préliminaires ont montrées les capacités de marquage de lipoplexes par de telles nanoparticules. / Silica nanoparticles are ideal platforms for the conception of bioimaging tools serving for the elucidation of the mechanisms of gene transfection via lipoplex structures. The purpose of the present study is the development of a chemical surface modification for the generation of quaternary ammonium groups on silica nanoparticles permitting the obtainment of highly positively charged silica colloids which strongly attract DNA by electrostatic interactions. Two modification strategies to generate quaternary ammonium groups on silica are presented a) a direct silanization using quaternary ammonium groups containing silane derivatives and b) a modification of silica nanoparticles via a first modification with an amine group containing silane derivative and a subsequent quaternization of the amine groups via an alkylation with iodomethane. Different physicochemical methods were employed (cosedimentation assays, quartz crystal microbalance with dissipation monitoring measurements, TEM and Cryo-TEM imaging) to analyze interactions between quaternized surfaces, DNA and lipids. A preliminary study was carried out which shows the capacity of the synthesized nanoparticles to label DNA in lipoplexes.

Protein (mis)folding into highly ordered, fibrillar structures, amyloid fibrils, is a hallmark of several, mainly neurodegenerative, disorders. The mechanism of this supra-molecular self-assembly reaction, as well as its relationship to protein folding are not well understood. In particular, the molecular origin of the metastability of the soluble state of proteins with respect to the aggregated states has not been clearly established. In this dissertation, it is demonstrated, that highly accurate kinetic experiments, using a novel biosensing method, can yield fundamental insight into the dynamics of proteins in the region of the free energy landscape corresponding to protein aggregation. First, a section on Method development describes the extension and elaboration of the previously established kinetic assay relying on quartz crystal microbalance measurements for the study of amyloid fibril elongation (Chapter 3). This methodology is then applied in order to study in great detail the origin of the various contributions to the free energy barriers separating the soluble state of a protein from its aggregated state. In particular, the relative importance of residual structure, hydrophobicity (Chapter 4) and electrostatic interactions (Chapter 5) for the total free energy of activation are discussed. In the last part of this thesis (Chapter 6), it is demonstrated that this biosensing method can also be used to study the binding of small molecules to amyloid fibrils, a very useful feature in the framework of the quest for potential inhibitors of amyloid formation. In addition, it is shown that Thioflavin T, to-date the most frequently employed fluorescent label molecule for bulk solution kinetic studies, can in the presence of potential amyloid inhibitor candidates be highly unreliable as a means to quantify the effect of the inhibitor on amyloid formation kinetics. In summary, the work in this thesis contributes to both the fundamental and the applied aspects of the field of protein aggregation.

Ce travail de thèse a été réalisé, dans le cadre de la convention CIFRE 1538/2010, au sein d'adixen Vacuum Products (aVP) à Annecy (France). Il a été en partie financé par le projet S.P.A.M. (Surface Physics for Advanced Manufacturing). Il s'agit d'un projet ITN financé par le programme Pierre et Marie Curie de la Communauté Européenne rassemblant des partenaires universitaires et industriels dont aVP. L'objectif de ce programme était de contribuer à l'étude et au développement de la lithographie et en particulier la lithographie à ultraviolet extrême (EUVL). Ce travail porte sur la problématique de la contamination moléculaire dans l'industrie des semi-conducteurs ainsi que les besoins de maitrise de contamination pour la photolithographie EUVL. Pour ce faire, des modèles mathématiques de sorption ont été recherchés, testés et validés à l'aide d'une microbalance à quartz (QCM). Cette technique, possédant une très haute sensibilité (au niveau du ng), permet d'étudier les phénomènes de sorption relatifs à tout matériau déposable sur un cristal de quartz mis au contact de différents gaz dont la pression partielle est maitrisée. Par conséquent, le protocole détaillé dans cette thèse peut être utilisé pour d'autres types d'expériences dans toute discipline nécessitant une telle précision. Le déroulement de notre plan d'expérience comprend deux types de matériaux naturellement différents : un polymère (PCBA) d'une part et deux substrats métalliques (SS AISI 304 et CuC1) d'autre part pour lesquels le transfert de masse n'intervient pas de la même manière. Les gaz d'étude ont été sélectionnés pour leur intérêt dans l'industrie des semi-conducteurs (vapeur d'eau, HF). Le résultat de l'interaction des gaz d'étude avec les substrats ciblés est suivi en direct par la QCM, ce qui permet non seulement de valider et/ou améliorer les modèles mathématiques déjà disponibles dans la bibliographie mais aussi de les ajuster aux données obtenues expérimentalement. Nous pouvons ainsi non seulement prévoir le comportement des contaminants à l'équilibre (isothermes) et à l'état transitoire mais aussi réaliser des estimations de sorption à des températures autres que celles retenues pour notre plan d'expérience / This thesis was carried out within the framework of the CIFRE 1538/2010 convention at adixen Vacuum Products (aVP) in Annecy (France). It is has been partly funded by the ITN project SPAM (Surface Physics for Advanced Manufacturing). SPAM is an ITN project funded by the Pierre and Marie Curie program of the European Community bringing together academic institutions and industrial partners including aVP. The objective of this program was to contribute to the study and development of lithography and extreme ultraviolet lithography (EUVL). This work deals with the issues caused by the airborne molecular contamination (AMC) in the semiconductor industry and their control needs in EUVL and the current photolithography. In order to tackle the problem, sorption mathematical models have been investigated and validated using a quartz crystal microbalance (QCM). This technique, which confers a high sensitivity (ng level), allows the study of the sorption phenomena related to any deposable material onto a quartz crystal in contact with different gases whose concentrations are accurately controlled. Consequently, the protocol detailed in this thesis may be used for other types of experiments in any discipline requiring such precision. The conduct of our experimental plan includes two types of naturally different materials: a polymer (PCBA) on the one hand and two metallic substrates (stainless steel AISI 304 and CuC1) on the other hand, for which the matter transfer does not occur in the same manner. Studied gases were selected for their interest in the semiconductor industry (water vapor, HF). The resulting interaction between the studied gases and the targeted substrates is continuously followed by the QCM, which allows not only to validate the mathematical models already proposed by the literature but also to fit the experimentally obtained data. This enables us not only to predict the behavior of the AMC at equilibrium (isotherms) and the transient state but also to provide sorption estimations at temperatures other than those specified in our experimental plan

Byl studován kontakt mezi koulí a deskou pod tangenciálním zatížením ve vodě. Jako zdroj střižných kmitů byl použit akustický rezonátor (křemíkové mikrováhy – QCM). Kontakt koule s povrchem resonátoru indukuje změnu resonanční frekvence a šířky pásma. Byla měřena změna frekvence f a změna šířky pásma v závislosti na amplitudě oscilací. S rostoucí amplitudou docházelo k poklesu f a růstem , což je chování typické pro parciální skluz. Díky aplikaci Cattaneo-Mindlinova modelu byl vypočítán kontaktní poloměr a třecí koeficient. Kontaktní poloměr při nízké amplitudě stoupal při zvětšujícím se normálovým zatížením. Tato závislost se dobře shodovala s JKR modelem. Třecí koeficient se nacházel v odpovídajícím rozsahu. Při zvyšování externí normálové síly, docházelo k nepatrnému snižování hodnoty třecího koeficientu. Toto chování je vysvětleno příspěvkem adhezivních sil k totální normálové síle. Výpočtem byly získány dva typy třecích koeficientů, první ze změny frekvence f a druhý ze změny šířky pásma . Tyto dvě hodnoty se spolu shodovaly z ± 20 % pro měření prováděná ve vodě, zatímco pro dvě měření prováděných na hydrofilním povrchu ve vzduchu se lišila. Tento nesoulad poukazuje na nedostatek Cattaneo Mindlinovy teorie a mohl by být vysvětlen přítomností kapilárních sil.

The Gram-negative bacterium Pseudomonas aeruginosa is a life-threatening nosocomial pathogen due to its generally low susceptibility toward antibiotics. Furthermore, many strains have acquired resistance mechanisms requiring new antimicrobials with novel mechanisms to enhance treatment options. Proline-rich antimicrobial peptides, such as the apidaecin analog Api137, are highly efficient against various Enterobacteriaceae infections in mice, but less active against P. aeruginosa in vitro. Here, we extended our recent work by optimizing lead peptides Api755 (gu-OIORPVYOPRPRPPHPRL-OH; gu = N,N,N′,N′-tetramethylguanidino, O = L-ornithine) and Api760 (gu-OWORPVYOPRPRPPHPRL-OH) by incorporation of Ile-Orn- and Trp-Orn-motifs, respectively. Api795 (gu-O(IO)2RPVYOPRPRPPHPRL-OH) and Api794 (gu-O(WO)3RPVYOPRPRPPHPRL-OH) were highly active against P. aeruginosa with minimal inhibitory concentrations of 8–16 and 8–32 μg/mL against Escherichia coli and Klebsiella pneumoniae. Assessed using a quartz crystal microbalance, these peptides inserted into a membrane layer and the surface activity increased gradually from Api137, over Api795, to Api794. This mode of action was confirmed by transmission electron microscopy indicating some membrane damage only at the high peptide concentrations. Api794 and Api795 were highly stable against serum proteases (half-life times >5 h) and non-hemolytic to human erythrocytes at peptide concentrations of 0.6 g/L. At this concentration, Api795 reduced the cell viability of HeLa cells only slightly, whereas the IC50 of Api794 was 0.23 ± 0.09 g/L. Confocal fluorescence microscopy revealed no colocalization of 5(6)-carboxyfluorescein-labeled Api794 or Api795 with the mitochondria, excluding interactions with the mitochondrial membrane. Interestingly, Api795 was localized in endosomes, whereas Api794 was present in endosomes and the cytosol. This was verified using flow cytometry showing a 50% higher uptake of Api794 in HeLa cells compared with Api795. The uptake was reduced for both peptides by 50 and 80%, respectively, after inhibiting endocytotic uptake with dynasore. In summary, Api794 and Api795 were highly active against P. aeruginosa in vitro. Both peptides passed across the bacterial membrane efficiently, most likely then disturbing the ribosome assembly, and resulting in further intracellular damage. Api795 with its IOIO-motif, which was particularly active and only slightly toxic in vitro, appears to represent a promising third generation lead compound for the development of novel antibiotics against P. aeruginosa.

The investigations are related to the influence of nonionic polyethoxylated surfactant on Tin- and Tin-Silver depositions. Cyclovoltammetry, electrochemical depositions in Hull cell, with quartz crystal microbalance, impedance spectroscopy, X-ray diffraction, REM and others were used as methods of characterization. / Die Untersuchungen befasssen sich mit dem Einfluss von nichtionischen polyethoxylierten Tenside auf die Zinn- und Zinn-Silber-Abscheidung, die durch Zyklovoltammetrie, Abscheidungen in der Hullzelle, mit der elektrochemischen Quarzmikrowaage, der Impedanzspektroskopie, Röntgendiffraktometrie, Rasterelektronenmikroskopie und Tensiometrie charakterisiert wurden.