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.

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.

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.

The subject of this thesis is the investigation of organic microcavities with implemented unstructured and laterally structured metal layers. The optical properties are studied by means of various spectroscopic techniques and are compared to conventional metal-free devices. It is shown that the large expected absorption caused by the embedded metal is reduced compared to the case of a free-standing metal layer of the same thickness. As a consequence of the interaction of the photonic cavity mode with the metallic structures, two new coupled modes emerge which are called Tamm plasmons. The strength of this coupling and the resulting spectral difference of these modes are defined by the thickness of both the metal layer and the adjacent dielectric layers. These control parameters enable the optimization of the structural design. Accordingly, coherent emission from Tamm plasmons is realized at room temperature. An analytical approach is developed accounting for the experimentally observed polarization splitting of detuned resonances. Next, laterally structured metal layers embedded into organic microcavities are considered. The structuring leads to a confinement of the photonic density of states evident from a clear discretization in energy of the corresponding modes. Applying a photolithographic technique to structure the metal layer into a pattern of regularly placed stripes leads to additional effects due to the resulting periodicity. By exciting this hybrid structure above a certain threshold, periodic arrays of localized cavity modes and metal-based Tamm plasmons are generated. These Bloch-like excited states are capable of phase coupling across the grating. Additionally, surface plasmon polaritons (SPPs) are excited propagating at the interface of the silver and the adjacent dielectric layers. Thanks to the periodicity of the metallic stripes, SPPs are subject to efficient Bragg scattering into the light cone in air. Modes up to order number 30 are detectable as quasi-linear periodic lines in the dispersion pattern. A Fourier analysis reveals an in- or out-of-phase coupling of the modes and a spread of the coherence over macroscopic distances of more than 40 µm. This strategy of embedding metal patterns into an organic microcavity yields a viable route towards electrically contacted organic solid-state lasers. / In dieser Arbeit werden erstmals dünne, unstrukturierte sowie lateral strukturierte metallische Schichten in organische Mikroresonatoren eingebettet und anschließend die optischen Eigenschaften mittels spektroskopischer Verfahren untersucht. Es zeigt sich, dass die erwarteten hohen optischen Verluste durch die Absorption des elektrischen Feldes im Metall deutlich reduziert sind, verglichen mit dem Fall einer freistehenden, nicht eingebetteten Metallschicht gleicher Dicke. Als Folge der Wechselwirkung der photonischen Kavitätsmode mit dem Metall spaltet diese in zwei miteinander gekoppelte Moden auf. Diese neuartigen Moden werden als Tamm-Plasmonen bezeichnet. Die Kopplung sowie die spektrale Differenz beider Moden ist zum einen durch die optischen Eigenschaften und die Dicke der eingebetteten Metallschicht definiert, zum anderen durch die optische Dicke der angrenzenden dielektrischen Schichten. Dadurch ist eine Optimierung des Systems im Hinblick auf Absorption und Emissionswellenlänge der Bauteile möglich, so dass selbst bei Raumtemperatur kohärente Emission eines Tamm-Zustands erzielt werden kann. Eine erarbeitete analytische Rechnung bestätigt und erklärt die experimentell gemessene, polarisationsabhängige Aufspaltung der auftretenden resonanten Moden. Im zweiten Teil der Arbeit sind organische Mikroresonatoren, deren eingebettete Metallschicht in lateraler Richtung auf verschiedene Weisen strukturiert sind, Gegenstand der Untersuchungen. Als Folge dieser Strukturierung kommt es zur lateralen Beschränkung der photonischen Zustandsdichte, was durch eine Diskretisierung der Energiespektren der resultierenden optischen Moden experimentell nachweisbar ist. Werden periodische Metallstreifen mittels Photolithographie erzeugt, so kommt es neben einer weiteren Beeinflussung der Zustandsdichte auch zu Effekten, die durch diese Periodizität bedingt sind. Entsprechend reproduziert sich die Kavitätsmode mehrfach im Impulsraum. Oberflächenplasmonen, die auf der Grenzfläche zwischen dem Metall und den dielektrischen Schichten propagieren, werden auf Grund der Periodizität bis in den experimentell zugänglichen Lichtkegel gestreut. Dabei werden Plasmonenresonanzen bis hin zur 30. Ordnung gemessen. Im letzten Experiment werden derart periodisch strukturierte Metall-Organik-Mikroresonatoren auf ihre Lasertätigkeit hin untersucht. Eine lokal begrenzte optische Anregung mittels eines gepulsten Lasers führt zur Ausbildung verschiedener Bloch-ähnlicher Moden, deren Kohärenz sich lateral bis zu 40 µm ausbreitet. Eine Fourieranalyse zeigt eindeutige und feste Phasenbeziehungen zwischen angrenzenden Maxima der Moden. Zusammenfassend ergeben sich interessante metall-organische Systeme, die minimale Absorption und niedrige Laserschwellen aufweisen und die prinzipielle Eignung zur elektrischen Kontaktierung besitzen.

"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.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 177-181).

IgM monoclonal gammopathy is a common age-related demyelinating sensory and motor polyneuropathy. It has been shown to be associated with antibodies against myelin-associated glycoproteins (MAG/SGPG). The HNK-1 carbohydrate epitope is a terminal 3-sulfo-glucuronyl residue attached to lactosamine structures and it is shared both in MAG and SGPG (SO4-3-GlcA(β1-3)Gal-(β1-4)GlcNAc(β1-3)Gal-(β1-4)Glcβ(1-1′)Cer). It is mostly expressed in the nervous system and plays an important role in preferential motor reinnervation. Nevertheless, the HNK-1 epitope is difficult to be isolated and synthesized and diagnostic assays used in the clinics are not always reproducible and reliable. Therefore in our study, our goal is to identify a simple synthetic diagnostic tool (peptide or monosaccharide), mimetic of the HNK-1 epitope, able to recognize antibodies in neurogammopathies sera by Surface Plasmon Resonance to be used in earlier stage patients and possibly to monitor disease activity. For this reason, we firstly tried to synthesize this trisaccharide and then we achieved the synthesis of its terminal monosaccharides with different function groups (octyl glucopyranoside, octyl glucuronic acid, octyl 3-O-sulfo-glucuronic acid and 8-amino octyl 3-O-sulfo-glucuronic acid). Then 10 linear and cyclic peptides conformationally and/or structurally mimicking HNK-1 were also synthesized (LSETTI, LSETTl, cyclo(-TTILSE-), cyclo(-TTlLSE-), cyclo(-TKTlLSE-), cyclo(-TETKlLSE-), TYTKlLSE, TY(SO3)TKlLSE, cyclo(-TYTKlLSE-) and cyclo(-TY(SO3)TKlLSE-)). The SPR kinetic binding affinities of all these sugar and peptide mimics were studied with commercial anti HNK-1 antibody using Biacore. Moreover, mimics with highest binding affinities were chosen for antigen-antibody interaction study in IgM gammopathy patients' serum.