This thesis concerns the development of surface ligation techniques for the preparation of carbohydrate biosensors. Several methodologies were developed based on efficient photochemical insertion reactions which quickly functionalize polymeric materials, with either carbohydrates or functional groups such as alkynes or alkenes. The alkyne/alkene surfaces were then treated with carbohydrate azides or thiols and reacted under chemoselective Cu-catalyzed azide-alkyne cycloaddition (CuAAC) or photo-radical thiol-ene/yne click chemistry, thus creating a range of carbohydrate biosensor surfaces under ambient conditions. The methodologies were evaluated by quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) flow through instrumentations with recurring injections of a range of lectins, allowing for real-time analysis of the surface interactions. The developed methods were proven robust and versatile, and the generated carbohydrate biosensors showed high specificities and good capacities for lectin binding.  The methods were then used to investigate how varying the glycan linker length and/or a sulfur-linkage affect the subsequent protein binding. The survey was further explored by investigating the impact of sulfur in glycosidic linkages on protein binding, through competition assays with various O/S-linked disaccharides in solution interactions with lectins. / QC 20120309

The aims of this study are to first immobilize positively charged gold nanorods to negatively charged cell culture surfaces. Second, to use polyelectrolytes for controlling the distance between gold nanorods and fluorophores. This is used to optimally determine the distance, of which maximum fluorescence enhancement is achieved, between gold nanorods and fluorophores. In order to approach these aims, we use UV/VIS absorption spectroscopy, fluorescence spectroscopy, atomic force microscopy, and ellipsometry. The results show that we could control the immobilization of gold nanorods on plastic microwell plates and create reproducible polyelectrolyte layers, in order to control the distance between the gold nanorods and fluorophores. In addition, the localized surface plasmon resonance wavelength red shifted as the PELs increased. In conclusion, we found that the maximum fluorescence enhancement of the fluorophores (Cy7) is about 2.3 times at a fluorophores-nanoparticles separation of approximately 9-12 nm. This work contributes some research information towards the design of optical biochip platforms based on plasmon-enhanced fluorescence.

Les métamatériaux sont des composites artificiels présentant des propriétés électromagnétiques qu'on ne trouve pas dans la nature. Malgré des développements spectaculaires durant la dernière décennie, le potentiel de ces structures aux longueurs d'ondes optique n'est pas encore clairement défini en raison de problèmes technologiques et de contraintes physiques telles que les pertes dans les métaux entrant dans la composition des métamatériaux. Dans notre thèse, nous montrons que les métamatériaux ont des propriétés très favorables dans le contexte de l'optique intégrée dans le proche infrarouge. Nous avons développé une stratégie pour incorporer des métamatériaux dans des circuits photoniques qui n'absorbent que très peu d'énergie. Pour cela, nous ne faisons pas directement agir l'ensemble du mode guidé avec les métamatériaux, mais seulement une composante évanescente à l'extérieur du guide. Pour réaliser un tel adaptateur ou d'autres fonctionnalités, il importe de déterminer quelle géométrie de métamatériaux est la plus favorable aux applications infrarouges. Nous proposons d'utiliser des structures à base de fils d'or empilés couche sur couche. A l'aide de simulations numériques et d'expériences en espace libre, nous montrons qu'il est possible d'obtenir toute une gamme de réponses optiques en contrôlant le couplage entre les différents niveaux de fils, c'est-à-dire en ajustant la distance entre les fils ainsi que leur alignement. En particulier, nous avons réussi à contrôler séparément la réponse électrique et magnétique de nos structures, ce qui offre une flexibilité de conception qui ne se rencontre pas dans les métamatériaux proposés jusqu'à présent.

Recently, technological advancement and the promise of next-generation devices have created an overwhelming push for the continued miniaturization of active systems to the micro- and nanometer scale. In this regime, traditional mechanical systems are largely inaccessible and as a result new active or stimuli-responsive materials are required. The work presented in this dissertation provides an understanding of the responsive nature of polymer and biopolymer interfaces especially in contact with metal nanoparticles. This understanding was utilized in conjunction with top-down template-based and self-assembly fabrication strategies to create hybrid protein based films and active polymer-metal hybrids that exhibit large and well-defined modulation of mechanical and optical properties. These materials processing developments represent advancement in the current state of the art specifically in three major areas: 1. template-based top-down control of protein chain conformation, 2. high-throughput synthesis and assembly of strongly coupled plasmonic nanoparticles with modulated optical properties (both near- and far-field), 3. field-assisted assembly of highly mobile and non-close packed magnetic nanorods with capabilities for rapid actuation.

Ce travail de thèse s'intéresse à deux types de matériaux composites en couches minces, dont les constituants sont des nanostructures de forme donnée faites de métal noble ; ils présentent des résonances de plasmon multipolaires. Leurs propriétés optiques dans le spectre visible-proche IR sont étudiées par deux techniques, le calcul par la méthode des éléments finis et l'ellipsométrie généralisée. Le premier type de matériau est le réseau de résonateurs en " U " faits d'or. Les mesures de matrices de Mueller par ellipsométrie permettent de mettre en évidence deux propriétés optiques particulières de ce type d'échantillon : d'une part le couplage magnéto-électrique et d'autre part la dispersion spatiale ; ces deux effets compliquent la description des propriétés optiques d'un matériau. Nous montrons dans un deuxième temps que ce type d'échantillon peut être décrit par un modèle effectif défini par des tenseurs constitutifs de permittivité, perméabilité et chiralité, malgré la dispersion spatiale. L'effet des résonances de plasmon multipolaires est exprimé par des oscillateurs de Lorentz. L'ajustement des paramètres d'un modèle effectif permet de définir complètement les propriétés optiques effectives d'un réseau de résonateurs en " U ". Le second type de matériau est un réseau désordonné de résonateurs hélicoïdaux faits d'argent. L'intérêt principal réside dans l'aspect industrialisable du process de réalisation ; l'inconvénient vient du caractère non-idéal des nanohélices. Nous montrons que ce type d'échantillon présente une dispersion spatiale très forte, mais que les résonances propres observés grâce au calcul par éléments finis sont utilisables pour les métamatériaux.

There is a high demand for quadruplex-specific compounds that not only bind preferentially to quadruplex DNA over duplex DNA, but also bind to one quadruplex motif over other motifs. Quadruplex structures are recognized as common occurrences in cancer cells, and if a compound could stabilize this structure, it may serve as an effective anti-cancer treatment with minimal side effects. In this study, cyanine dyes’ interactions with DNA were analyzed with fluorescence titrations, UV-Vis thermal studies, circular dichroism titrations, and surface plasmon resonance (SPR) analysis. With these techniques, binding affinity, DNA stabilization, and conformational shifts were analyzed to determine if cyanine dyes could act as quadruplex-specific binding compounds for possible cancer treatments.

"There is plenty of room at the bottom." This bold and prophetic statement from Nobel laureate Richard Feynman back in 1950s at Cal Tech launched the Nano Age and predicted, quite accurately, the explosion in nanoscience and nanotechnology. Now this is a fast developing area in both science and technology. Many think this would bring the greatest technological revolution in the history of mankind. To understand electronic and optical properties of nanostructures, the following problems have been studied. In particular, intensity of mid-infrared light transmitted through a metallic diffraction grating has been theoretically studied. It has been shown that for s-polarized light the enhancement of the transmitted light is much stronger than for p-polarized light. By tuning the parameters of the diffraction grating enhancement can be increased by a few orders of magnitude. The spatial distribution of the transmitted light is highly nonuniform with very sharp peaks, which have the spatial widths about 10 nm. Furthermore, under the ultra fast response in nanostructures, the following two related goals have been proved: (a) the two-photon coherent control allows one to dynamically control electron emission from randomly rough surfaces, which is localized within a few nanometers. (b) the photoelectron emission from metal nanostructures in the strong-field (quasistationary) regime allows coherent control with extremely high contrast, suitable for nanoelectronics applications. To investigate the electron transport properties of two dimensional carbon called graphene, a localization of an electron in a graphene quantum dot with a sharp boundary has been considered. It has been found that if the parameters of the confinement potential satisfy a special condition then the electron can be strongly localized in such quantum dot. Also the energy spectra of an electron in a graphene quantum ring has been analyzed. Furthermore, it has been shown that in a double dot system some energy states becomes strongly localized with an infinite trapping time. Such states are achieved only at one value of the inter-dot separation. Also a periodic array of quantum dots in graphene have been considered. In this case the states with infinitely large trapping time are realized at all values of inter-dot separation smaller than some critical value.

The development of small-molecules which target nucleic acids, more specifically the minor groove of DNA, in a sequence specific manner and control gene expression are currently being investigated as potential therapeutic compounds for the treatment of various diseases, including cancer, as well as viral and bacterial infections. The naturally occurring compounds netropsin and distamycin have been shown to demonstrate antitumor and antibacterial properties. Currently, there are synthetic efforts to create pyrrole and imidazole-containing polyamide derivatives of netropsin and distamycin that show potential as medicinal agents. Synthetic pyrrole and imidazole-containing polyamides are potentially useful for targeting and modulating the expression of genes, including those associated with cancer cell growth. The key challenges that must be overcome to realize this goal of using synthetic polyamides in the treatment of disease are the development of polyamides with low molar mass so the molecules can readily diffuse into cells and concentrate in the nucleus. In addition, the molecules must have appreciable water solubility, bind DNA sequence specifically, and with high affinity. As part of a systematic study within the authors’ laboratory, our goal is to develop polyamides which can be synthesized readily yet possess excellent sequence specificity, stronger binding affinity, high solubility in biological media and enhanced cell penetration and nuclear localization properties. There is a need to develop a library of modified polyamides which target DNA and exhibit improved biological properties. The present study is a systematic examination of the binding properties of various modified synthetic polyamide compounds. The synthetic polyamide derivatives presented have more potential as therapeutic candidates over other synthetic polyamides because of their increased water solubility, smaller molecular weights, and molecular design, thus, allowing them to penetrate into cells and localize in the nucleus.

Reliable analytical tools are important for time efficient and economical process development, production and batch release of pharmaceuticals. Therapeutics recovered from human plasma, called plasma protein products, involve a large pharmaceutical industry of plasma fractionation. In plasma fractionation of human immunoglobulin G (hIgG) and albumin (HSA) recommended analysis techniques are regulated by the European Pharmacopoeia and are including total protein concentration assays and zone electrophoresis for protein composition and purity. These techniques are robust, but more efficient techniques with higher resolution, specificity and less hands-on time are available. Surface plasmon resonance is an optical method to study biomolecular interactions label-free in real time. This technology was used in this master thesis to set up assays using Biacore systems for quantification of HSA and hIgG from all steps of chromatographic plasma fractionation as a tool for process development and in-process control. The analyses have simplified mass balance calculations to a high extent as they imply specific detection of the proteins compared with using total protein detection. The assays have a low hands-on time and are very simple to perform and the use of one master calibration curve during a full week decreases analysis time to a minimum. Quick, in-process control quantification of one sample is easily obtained within <10 minutes. For final QC of hIgG or for process development, an assay to quantify the distribution of the IgG subclasses (1-4) was set up on Biacore and showed significantly lower hands-on time compared with a commercial ELISA. All assays showed reliable quantification and identification performed in unattended runs with high precision, accuracy and sensitivity.

Biodegradable, edible wheat gluten films offer a renewable alternative to plastic food packaging or can be incorporated directly in the food product. Wheat gluten is a good option because it forms a fibrous network, lending strength and elasticity to films. The goal of this research project was to produce, with a water-based film formulation and methodology, smooth, homogeneous wheat gluten films with low water vapour permeability (WVP). The water-based film formulation also served to compare the FT Wonder wheat cultivar, grown in Ontario, to commercially produced wheat gluten and determine the effect of wheat source on the film properties, surface morphology, surface hydrophobicity, WVP, and film swelling in water for different pH, temperature and casting surface conditions. Fluorescence, SPR, and casting formulation viscosity provided preliminary information on the mechanism of film formation and on gluten protein structure induced by modifying the film formulation. This research provides an alternate use for some Ontario wheat cultivars based on their properties in films compared to commercial sources of gluten. As a result, using Ontario cultivars to prepare gluten film packaging material has potential as an alternate source of income for Ontario farmers. This research also defines the film properties for gluten films produced from aqueous solutions, helping to identify processing parameters that could bring gluten films on par with plastic packaging and make gluten films a viable alternative food packaging material. Finally, it was determined that the water vapour permeability of wheat gluten films was not correlated to film surface contact angle.