In this project a method based on surface plasmon resonance has been developed for determining the concentration of several His-tagged proteins in complex solutions. It showed large dynamic range, no measureable non-specific binding and high sensitivity (with linear range around 0.1–10 μg/ml depending on the proteins). The method showed a low variation when checked on MBP-His during an extended time period. The concentrations of the His-tagged protein in the lysate has also been determined and compared with other alternative methods. This method will later be used to analyse protein concentrations during development and optimization of chromatographic purification process.

No description available.

Surface plasmons are bound TM polarized electromagnetic waves that propagate along the interface of two materials with real dielectric constants of opposite signs. Surface plasmon resonance (SPR) sensors make use of the surface plasmon waves to detect refractive index changes occurring near this interface. For sensing purposes, this interface typically consists of a metal layer, usually gold or silver, and a liquid dielectric. SPR sensors usually measure the shift in resonance wavelength or resonance angle due to index changes adjacent to the metal layer. However this restricts the limit of detection (LOD), as the regions of low slope (intensity vs. wavelength or angle) in the SPR curve contain little information about the resonance. This work presents the technique of tunable laser interrogation of SPR sensors. A semiconductor laser with a typical lasing wavelength of 650nm was used. A 45nm gold layer sputtered on a BK7 glass substrate served as the sensor. The laser wavelength is tuned to always operate in the region of highest slope by using a custom-designed LabVIEW program. It is shown that the sensitivity is maximized and LOD is minimized by operating around the region of high slope on the SPR curve.

Surface immobilization of probe molecules in surface based assays is a key area of research in the continued development of immunoassay microarrays. Interest continues to grow in microarray based immunoassays given their potential as a high throughput technique for immunodiagnostics. Therefore, it is important to thoroughly study and understand the implications of interfacial chemistry and immobilization conditions on the performance of the assay. This thesis presents a body of work that examines the impact of probe density, interfacial chemistry, and enhancement factors for arrays read with surface plasmon resonance (SPR) imaging. An array of structurally similar Salmonella disaccharides was immobilized at varying densities and the interface formed was thoroughly investigated to determine the properties of the interface. The arrays were then used with SPR imaging to evaluate the binding of an antibody specific for one disaccharide of the three stereoisomers on the array. A dilute disaccharide surface was found to provide optimal antibody binding. Higher densities result in steric hindrance of antibody binding by not allowing the disaccharide to insert into the antibody binding pocket. The role of interfacial chemistry in antibody attachment was studied to determine optimum conditions. The study examined physical adsorption, covalent attachment, and affinity capture. It was found that covalent attachment provided the most stable attachment and resulted in the lowest levels of antigen detection. Both the physical adsorption and affinity capture provided larger antigen binding capacity and therefore more sensitive antigen detection. The covalent attachment was chosen to evaluate an enhanced assay with the incorporation of gold nanoparticles. These particles provided detection limits that were an order of magnitude improved over those excluding the nanoparticles. A novel surface chemistry for antibody immobilization in SPR imaging studies was evaluated. This involved the electrochemical driven formation of mono- to multilayers of diazonium benzoic acid films. The studies showed the ability to control the thickness of the films formed and also the ability of the antibody chips to capture antigen from solution.

No description available.

Plasmonics techniques, such as surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS), have been widely used for chemical and biochemical sensing applications. One approach to excite surface plasmons is through the coupling of light into metallic grating nanostructures. Those grating nanostructures can be fabricated using state-of-the-art nanofabrication methods. Laser interference lithography (LIL) is one of those methods that allow the rapid fabrication of nanostructures with a high-throughput. In this thesis, LIL was combined with other microfabrication techniques, such as photolithography and template stripping, to fabricate different types of plasmonic sensors. Firstly, template stripping was applied to transfer LIL-fabricated patterns of one-dimensional nanogratings onto planar supports (e.g., glass slides and plane-cut optical fiber tips). A thin adhesive layer of epoxy resin was used to facilitate the transfer. The UV-Vis spectroscopic response of the nanogratings supported on glass slides demonstrated a strong dependency on the polarization of the incident light. The bulk refractive index sensitivities of the glass-supported nanogratings were dependent on the type of metal (Ag or Au) and the thickness of the metal film. The described methodology provided an efficient low-cost fabrication alternative to produce metallic nanostructures for plasmonic chemical sensing applications. Secondly, we demonstrated a versatile procedure (LIL either alone or combined with traditional laser photolithography) to prepare both large area (i.e. one inch2) and microarrays (μarrays) of metallic gratings structures capable of supporting SPR excitation (and SERS). The fabrication procedure was simple, high-throughput, and reproducible, with less than 5 % array-to-array variations in geometrical properties. The nanostructured gold μarrays were integrated on a chip for SERS detection of ppm-level of 8-quinolinol, an emerging water-borne pharmaceutical contaminant. Lastly, the LIL-fabricated large area nanogratings have been applied for SERS detection of the mixtures of quinolone antibiotics, enrofloxacin, an approved veterinary antibiotic, and one of its active metabolite, ciprofloxacin. The quantification of these analytes (enrofloxacin and ciprofloxacin) in aqueous mixtures were achieved by employing chemometric analysis. The limit of quantification of the method described in this work is in the ppm-level, with <10 % SERS spatial variation. Isotope-edited internal calibration method was attempted to improve the accuracy and reproducibility of the SERS methodology. / Graduate / 2018-02-17

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

Surface plasmon waves are transverse magnetic electromagnetic waves propagating along a dielectric-metal interface. These waves can be excited by resonant absorption of electromagnetic radiation leading to surface plasmon resonance (SPR) at the interface. The resonance is characterised by a reduction in the intensity of the reflected light at the interface due to strong coupling of incident optical radiation to surface plasmons. This gives rise to a minimum at a sharply defined angle of incidence, referred to as SPR angle or plasmon angle. The phenomenon of SPR has been extensively used in the past to develop reflective type optical devices for sensing applications on account of the high dielectric function dependent sensitivity of the SPR angle. Basically, devices which exhibit this phenomenon have a structure consisting of a metal film sandwiched between two dielectrics. The reflectivity of such a device is theoretically modelled based on either theory of thin films (Fresnel's model) or theory of resonance (Lorentzian model). These models have very effectively predicted the behaviour of such devices based on the shift in SPR angle due to the dielectric function variations. We have been investigating the SPR device for intensity based metrological applications utilising its high angular sensitive reflectivity, with fixed SPR angle. In these intensity based applications or measurements, direct and simple expressions connecting intensity variation to angular change are unavailable in the literature and quantitative estimation or data inversion is based on either curve fitting or iterative methods. Fresnel and Lorentzian models have commonly been used in the experiments but data inversion through the Fresnel model is computationally complex and the Lorentzian model, although less complicated, gives erroneous results due to its approximate nature. In order to obtain a simple expression between intensity variation and the angular change, we have re-looked at the two existing models in order to derive an expression which has the simplicity of the Lorentzian model and the accuracy of the Fresnel model in the experiments with fixed plasmon angles. These efforts have been particularly directed to understand the relationship between intensity variation and meteorologically important properties of such devices. This thesis is an attempt to summarize the computational results which have led us to some novel experimental methodologies which have been used to exploit these devices for inverse type, illumination specific, SPR based applications. The work presented in this thesis is organised in six chapters. Chapter 1, gives an overview of optical sensing, theory of surface plasmons, excitation schemes for surface plasmons, development of the SPR device and its characterisation. It also includes a brief literature review in the area of surface plasmon resonance, covering both the theoretical and experimental aspects. The objectives of the work and the scope of the thesis are also presented. Chapter 2 presents the existing models of SPR device, based on Fresnel's and the Lorentzian models. These models allow reflectance calculations from knowledge of either the optical parameters that describe the layers or the parameters of the waves that propagate through them. Using these models, the inverse problem of estimating either the angle of incidence or the optical constants of the layers of the sensors utilizing the intensity based measurements is generally difficult. In order to solve this problem where the plasmon angles are fixed, a modified formalism for the angle scanned SPR spectrum of a three-layered SPR sensor is presented in this chapter. The new formalism regroups the wave vector parameters of Lorentzian resonance theory into a set of non-dimensional parameters 1, 4K and R. The new reflectivity index (1), which is the ratio of reflectance to the absorptance, has been introduced to help explain the physical processes underlying the device operation in the high sensitivity region of the characteristics. The parameter 4Kis a constant of the device and it depends on the dielectric constants of the device. This is a new SPR index and is identified at a point where reflectance and absorptance match. Parameter R is related to the loss mechanisms in the device and will be explained in detail in Chapter 3. This simple model links the new reflectivity index (1) to the angular detune from SPR angle (ΔƟ) and it brings out a parabolic variation of ΔƟ with 1. In this chapter the mathematical derivation of the proposed model is presented and the significance of the new parameters 1, 4Kand Rare discussed. Chapter 3 evaluates the characteristic nature of errors associated with the predictions from the proposed model and presents methods for neutralizing them. It is demonstrated with the help of the function K which is linearly dependant on 1, that the proposed model predicts the reflectance from the wave vector parameters as accurately as the Fresnel's model. This R parameter explains the slowly varying nature of the radiative loss with the angle of incidence and this variation contributes significantly to the SPR characteristics. As a consequence, it is found that the SPR characteristics can be represented as a sum of two primary functions which are parabolic and linear, respectively, and this leads to the easy explanation of the SPR characteristics. The present chapter also discusses a new observation that the angle-scanned SPR spectrum can be accurately described using a straight line in intercept form. The intercept value depends on 4Kand the slope depends on K. In addition to this, this chapter discusses practical methods for estimation of the intercept and the slope of such a straight line which are functions of the key wave vector parameters. A detailed discussion on the proposed model highlighting its advantages for inverse type, illumination specific, SPR-based applications with fixed SPR angle is also presented. Chapter 4 describes the applications of the proposed model for optical constant measurements. The first part highlights a new approach for the determination of the dielectric constants of the metal film used for the optimised- or nearly-optimised SPR sensors using the proposed model. In the complex dielectric constant, the real part is calculated from the SPR angle and the imaginary part from 4K. A discussion on the dielectric constant study of silver and gold metal film is presented. The advantages of the proposed approach such as its simplicity and direct methodology are then discussed. The second part of the chapter also proposes a new approach to carry out measurements on the absorbance of the medium with enhanced sensitivity utilising the parameter 4K It describes a computational study on the variation of 4K values with the dielectric function and highlights the relationship of 4K variation due to the imaginary part of the dielectric function (absorption) of the samples. The physical processes causing a change in the value of 4Kdue to absorption is also discussed along with some computational results. Chapter 5 reports the study carried out to bring out the importance of the new index,4K in metrological applications. Based on the new model, the effect of the laser beam divergence on SPR curve is studied. This chapter first of all discusses the design of the SPR device and the new methods for the development and characterisation of such a device. Details of the experimental procedure for laser divergence evaluation are proposed along with some of the significant computational results. Furthermore, a few applications such as focal length measurement of optical lenses, micro-displacement measurement based on the divergence of the laser beam are also reported. Since the SPR characteristics can be represented easily using the new model, the angular dependent intensity variation can be utilised for some metrological applications with simple data processing. In this context, the high angular sensitivity of the SPR device is studied and some applications such as micro-displacement measurement, pressure measurement and optical wedge angle measurement are included to highlight the above advantages. The last chapter, Chapter 6, gives a summary and conclusions of the work presented in the thesis. The scope for future investigations is also included in this chapter.

Recent advances in nanofabrication techniques have opened up new avenues and numerous possible applications in both nanoscale electrochemistry and analytical nanoscience by enabling the fabrication of reproducible nanoelectrodes with different new geometries. Nanoelectrodes exhibit advantages including enhanced mass transport, higher current densities, improved signal-to-noise ratios, and lower ohmic drop. In this dissertation, the use of nanoelectrodes in the electrochemical response properties investigations or in the spectroelectrochemical studies is the unifying factor among all the chapters. First (in Chapter 4), we presented a direct comparison between the electrochemical characteristics of two finite nanoelectrodes arrays with different geometries: 6 × 6 recessed nanodiscs and nanorings microarrays. Using computational methods, it was demonstrated that the electrode geometry’s parameters have a drastic influence on the mass transport properties of the nanoelectrodes. The results presented here are the first combination of experimental and numerical studies that elucidate the transport on nanoring electrode arrays. The comparison of the electrochemical behavior between nanostructures using full 3D simulations is also unique. Second, we have provided a comprehensive numerical study on the redox cycling performance properties of a 6 × 6 recessed nanorings-ring electrode array configuration. The simulation results were in good agreement with the experimental data. After validating the model against experiments, a comprehensive computational investigation revealed avenues to optimize the performance of the structure in terms of geometric parameters and scan rates. The second half of this dissertation is comprised of the spectroelectrochemical studies. The combination of surface plasmon resonance with electrochemistry presents new paths to investigateredox reaction events at the electrode surface since it brings an additional dimension to the classical electrochemical approaches. Third, we have reported a novel active plasmonic device based on a new switching mechanism for the nanohole electrodes array to bridge between photonics and electronics at nanoscales. The inner surfaces of the nanohole electrodes in the array were coated with an electroconductive polymer, polypyrrole, (PPy). Then, it was shown that light transmitted through the PPy- modified nanohole electrodes can be easily tuned and controled by applying an external potential. We were also able to switch on and off the transmitted light intensity through the modified nanohole arrays by potential steps, demonstrating the potential of this platform to be incorporated into optoelectronic devices. Finally, we have fabricated larger area plasmonic periodic nanopillar 3D electrodes using a rapid, high-throughput, and cost-effective approach: the laser interference lithography. Then, the electrochemical behavior of these electrodes was investigated both experimentally and computationally. The properties were ‘compared with a flat electrode with an equivalent geometric area. Afterward, we have successfully probed the changes in the concentration of a reversible redox pair near the electrode surface induced by various applied potentials, in an in-situ EC-SPR experiment. / Graduate

FGF2 (Fibroblast Growth Factor 2), o fundador da família FGF, tem funções regulatórias na mitogênese, diferenciação, morfogênese e reparo tecidual. Diversas espécies moleculares de FGF2 compartilham uma seqüência C-terminal comum de 155 aminoácidos, pois se originam de diferentes sítios de iniciação de leitura de um único mRNA. O menor, o FGF2-18kDa, é liberado extracelularmente para se ligar a receptores específicos (FGFRs) para disparar as funções parácrinas e autócrinas pelas quais este fator é conhecido. Por outro lado, as espécies maiores (FGF2-21, 22, 22,5 e 34kDa) são intracelulares se ligam a parceiros moleculares desconhecidos para exercer funções intrácrinas ainda indefinidas. O objetivo desta tese foi produzir espécies recombinantes do FGF2-18 e FGF2-22,5, na forma de proteínas de fusão, para analisar funções biológicas e mecanismos de sinalização. Nas células malignas Y1 de camundongo, os recombinantes de FGF2-18kDa (FGF2-18, His-FGF2-18 e His-FGF2-18-ProA) dispararam uma resposta antagônica estimulando as vias de sinalização mitogênica, mas bloqueando o ciclo celular. Nos fibroblastos não tumorigênicos Balb3T3, estes mesmos recombinantes de FGF2-18kDa dispararam apenas a resposta mitogênica clássica. Todos os efeitos biológicos destes recombinantes de FGF2-18kDa foram bloqueados pelo inibidor específico da proteína quinase de tirosina dos FGFRs, PD173074, demonstrando que são respostas intermediadas pelos FGFRs. Portanto, os domínios estruturais adicionados aos recombinantes de FGF2-18kDa não impediram que estas proteínas se ligassem e ativassem os FGFRs. Por outro lado, o recombinante His-FGF2-22,5 dispara apenas as vias de sinalização mitogênica em ambas as células Y1 e 3T3, mas este efeito biológico não é inibido por PD173074. Estes resultados sugerem que a seqüência N-terminal de 55 resíduos, rica em aminoácidos básicos, impede que o FGF2-22,5kDa se ligue e/ou ative os FGFRs. Entretanto, o recombinante His-FGF2-22,5ProA dispara a resposta antagônica característica do FGF2-18kDa. As implicações destes últimos resultados é que o domínio de ProA adicionado ao C-terminal torna o FGF2-22,5kDa um bom ligante dos FGFRs. A interação física entre ligante e receptor das formas recombinantes His-FGF2-18kDa (ou His-FGF2-18ProA) e FGF2-22,5kDa com os putativos FGFRs foi analisada através da técnica de SPR e os resultados mostram KDs aproximados (Kd18=21, 488.10-9 e Kd22,5=20,70393.10-9), enquanto que o número de sítios ligantes em vesículas microssomais das células é significantemente inferior para o FGF2-22,5kDa. Estes resultados são compatíveis com a existência de receptores diferentes para FGF2-18kDa e FGF2-22,5kDa, uma hipótese ainda a ser definitivamente corroborada. Em conclusão, o FGF2-18kDa, mesmo em formas recombinantes como proteína de fusão, dispara todos os efeitos biológicos descritos para FGF2, através dos FGFRs. Diferentemente, o FGF2-22,5kDa, como fator parácrino, só desencadeou a resposta mitogênica clássica de FGF2, provavelmente através de receptores diferentes dos FGFRs. Os resultados e conclusões desta tese têm um potencial indiscutivelmente relevante para a biologia molecular do câncer, com implicações possíveis em terapia oncológica / FGF2 (Fibroblast Growth Factor 2), the founder of the FGF family, has regulatory functions in mitogenesis, differentiation, morphogenesis and tissue repair. Multiple FGF2 molecular species, sharing a C-terminal sequence of 155 amino acids, are translated from different iniciation sites of the same mRNA. The smaller, the FGF2-18kD, is extracellularly released to bind to specific membrane receptors (FGFRs), performing paracrine and autocrine functions. On the other hand, the larger FGF2s (21, 22, 22.5 and 34kDa) are intracellular species that bind to unknown partners to play still undefined intracrine roles. The aim of this thesis was to produce recombinant species of FGF2-18kDa and FGF2-22,5kDa, in the form of fusion proteins, to analyze functions and signaling mechanisms. In mouse Y1 malignant cells, FGF2-18kD recombinants (FGF2-18kDa and His-FGF2-18kDaProA) triggered an antagonistic response activating mitogenic signaling pathways, but blocking the cell cycle. However, in non tumorigenic Balb3T3 fibroblasts, these same FGF2-18kD recombinants only elicited the classical mitogenic response. All biological effects of these FGF2-18kD recombinants were blocked by the specific inhibitor of FGFR-protein-tyrosine-kinases, PD173074, demonstrating that these responses are mediated by FGFRs. Therefore, the new peptide domains added to FGF2-18kD did not prevent these recombinant fusion proteins to bind and activate FGFRs. Conversely, the recombinant His-FGF2-22,5kDa triggered only mitogenic signaling pathways in both Y1 and Balb3T3 cells, a biological effect not inhibited by PD173074. These results suggested that the additional basic-rich N-terminal sequence of 55 amino acid residues, found in FGF2-22,5kDa, prevents this FGF2 species from binding and / or activate FGFRs. However, surprisingly, the recombinant His-FGF2-22kDaProA triggered the antagonistic response characteristic of FGF2-18kDa. These results imply that the ProA-domain added to the C-terminal end rendered the FGF2-22,5kDaProA a good ligand of FGFRs. The physical interaction between recombinants of both His-FGF2-18kD and His-FGF2-22kDa with putative FGFRs, analyzed by SPR, yielded close KD values (KD18=21, 5.10-9 e K D22,5=20,7.10-9), while the number of binding sites in cell microsomal vesicles were significantly lower for the His-FGF2-22,5kDa. These results are consistent with the existence of different receptors for FGF2 and FGF2-18kD-22,5kDa, a hypothesis that has yet to be definitively confirmed. In conclusion, FGF2-18kD, even as recombinant fusion proteins, triggered all biological effects of FGF2, through FGFRs. Conversely, the FGF2-22, 5kDa only triggered the classical mitogenic response, probably via receptors other than FGFRs. The results and conclusions of this thesis are potentially of great interest in cancer molecular biology, with implications in oncologic therapy.