The self-assembly of amyloidogenic proteins to form cytotoxic species that give rise to brain deterioration underlies numerous neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. Increasing evidence indicates that it is the rare, low-molecular-weight species (oligomers) rather than the more abundant high-molecular-weight fibrils of certain proteins that are the most cytotoxic in several neurodegenerative diseases. However, these species have proven difficult to study using traditional methods due to their transient nature and the heterogeneity of aggregation mixtures. In this thesis, I describe my work to develop advanced methods where I combine single-molecule and ensemble fluorescence techniques with microfluidic strategies to enable the study of protein aggregation, spanning small, transient oligomers to large, insoluble aggregates. In Chapter 1 I give an overview of the biological context and relevance of this work, including the background of neurodegenerative disease, amyloidogenic aggregation and key proteins involved. I then briefly review fluorescence microscopy techniques and the field of microfluidics. In Chapter 2 I describe how complex microfluidics can be integrated with single-molecule confocal techniques to provide a highly sensitive method to continuously probe protein aggregation in vitro. I show, for the first time, that the dilution of aggregating mixtures may be automated, by up to five orders of magnitude, down to the picomolar concentrations suitable for single-molecule measurements. By incorporating this microfluidic dilution device I greatly improve the temporal resolution of the technique and facilitate the observation of more transient species through the ability to rapidly dilute and take fluorescence measurements of samples. In Chapter 3 I overcome the need for in situ labels to monitor amyloidogenic aggregation using single-molecule confocal microscopy. I describe my work to adapt the single-molecule confocal technique to achieve the ultrasensitive detection of individual aggregate species under flow without covalently-attached labels. I have demonstrated the ability of this new method to monitor the aggregation of label-free amyloidogenic proteins using extrinsic labels ex-aggregation, opening the way for biological samples to be probed in a high-throughput manner. In Chapter 4 I describe my work to combine the high precision of confocal microscopy with a microfluidic device developed to directly characterise the sizes and interactions of biomolecules in the continuous phase. By monitoring the spatial and temporal mass transport on the micron scale, the diffusion coefficient, and thus hydrodynamic radius, of species may be determined. The technique delivers much greater sensitivity for size quantification, allowing scarce and other challenging samples to be characterised, and provides significant steps towards accurate sizing for single-molecule aggregation experiments under flow. In Chapter 5 I describe my work to determine the microscopic driving force for the spatial propagation of amyloid-beta. The epifluorescence instrument I built has enabled the proliferation of aggregate species to be monitored over a macro distance on a timescale of minutes. This has greatly improved the scope of the experimental data attained, which will be used in conjunction with Monte Carlo simulations to deliver a model for the propagation of amyloid-beta in vitro. Together this thesis represents my work developing the above novel fluorescence techniques to improve their temporal and size resolution, sensitivity and adaptability to study highly complex and fundamental protein aggregation linked to neurodegenerative disease.

The development of single-molecule and super-resolution fluorescence techniques has revolutionised biological imaging. Nano-scale cellular structures and heterogeneous dynamic processes are now able to be visualised with unprecedented resolution in both time and space. The achievable localisation precision and therefore the resolution is fundamentally limited by the number of photons a single-fluorophore can emit. The ideal super-resolution dye would emit a large number of photons over a short period of time. On the contrary, an optimal single-molecule tracking probe would be highly photostable and undergo no transient dark-state transitions. Single-molecule instrument development is beginning to reach technological saturation and as the frontiers of bioimaging expand, exorbitant demands are placed on the gamut of available probes that often cannot be met. Thus, the next key challenge in the field is the development of the better fluorophores that underlie these techniques; this includes both the synthesis of new chemical derivatives and alternative novel strategies to augment existing technologies. The results of this thesis are divided into two distinct parts; Project One details the development of new synthetic fluorescent probes for the study of amyloid protein aggregates implicated in neurodegenerative diseases. This includes a study of the photophysical and binding properties of a novel fluorophore library based on the amyloid dye Thioflavin-T. Following on from this, is the presentation of novel bifunctional dyes capable of simultaneously identifying hydrogen peroxide and amyloid aggregates by combining existing tools for the independent detection of these species. The sensing capabilities of these dyes are explored at the bulk and single-molecule levels. Project Two describes a new photo-modulatable fluorescent-protein fusion construct that can undergo Förster resonance energy transfer (FRET) to an organic dye molecule. This FRET cassette is comprised of a photoconvertible fluorescent protein donor, mEos3.2 and acceptor fluorophore, JF646. This strategy imparts a strong photostabilising effect on the fluorescent protein and a resistance to photobleaching. The functionality of this approach is demonstrated with in vitro single-molecule fluorescence studies and its biological applicability shown by tracking single proteins in the nuclei of live embryonic stem cells. Furthermore, initial characterisations of the excited state dynamics in effect are presented through the systematic modification of parameters.

This thesis is dedicated to the study of fluorescent conjugated polymers made of fluorene labelled with rylene moieties. Those polymers are important candidates for use in Organic Light Emitting Devices (OLEDs). The dyes present in the polymers were studied at the single-molecule level. The first part of the work is devoted to the construction and validation of an epi-fluorescent confocal/widefield/Total Internal Reflection microscope. The ensemble properties of the samples are first measured in solution. The combination of steady-state and time-resolved spectroscopies allows us to unravel the photophysics of the conjugated polyfluorene polymer containing perylenediimides in its backbone. Energy transfer is found to occur between the polyfluorene and the perylenediimide units. Beside energy transfer, a photoinduced electron transfer is also supposed to take place. Widefield microscopy is used to measure the end-to-end distance in single polymer chains. From those measurements the polymer is shown to present a quasi linear shape inside its host matrix. From the simulation of the end-to-end distance distribution, a conjugation length of 4-6 fluorene units is found. The introduction of a new subtraction method associated with defocused imaging allows us to study a more complicated polymer containing more perylenediimide units. The location and the 3D orientation of the incorporated dyes were measured at the same time by this new technique named SPIDER. Finally, the sequential two-color measurements allow us to get useful informations concerning the energy transfer occurring between polyfluorene backbone and perylenediimide units at the single molecule level.

Thesis (Ph. D.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 218-225). Also available on the World Wide Web.

This thesis will present the synthesis, characterization and magnetic measurements of lanthanide complexes with varying nuclearities (Ln, Ln2, Ln3 and Ln4). EuIII, GdIII, TbIII, DyIII, HoIII and YbIII have been selected as the metal centers. Eight polydentate Schiff-base ligands have been synthesized with N- and mostly O-based coordination environments which chelate 7-, 8- or 9-coordinate lanthanide ions. The molecular structures were characterized by single crystal X-ray crystallography and the magnetic properties were measured using a SQUID magnetometer. Each chapter consists of crystal structures and magnetic measurements for complexes with the same nuclearity. There are eight DyIII SMMs in this thesis which are discrete molecules that act as magnets below a certain temperature called their blocking temperature. This phenomenon results from an appreciable spin ground state (S) as well as negative uni-axial anisotropy (D), both present in lanthanide ions owing to their f electron shell, generating an effective energy barrier for the reversal of the magnetization (Ueff). The ab initio calculations are also included for the SMMs with high anisotropic energy barriers to understand the mechanisms of slow magnetic relaxation in these systems.

Stoichiometric and catalytic small molecule activation reactions are vital for the synthesis of new materials. The activation of phosphorus-hydrogen or phosphorus-phosphorus bonds allows for the facile synthesis of new phosphorus-containing molecules for a wide variety of applications.1 An investigation of the P-H dehydrocoupling reaction was undertaken utilizing two rhodium(I) based catalysts. Over the course of this investigation it was found that the Rh(I) systems were also active catalysts for the reverse reaction: phosphorus-phosphorus bond hydrogenation (and hydrosilylation). This reaction was exploited for the synthesis of novel phosphines from P-P bound species. Molecules with P-P bonds were reacted in a stoichiometric fashion with the catalyst precursor, producing a variety of novel species with interesting bonding features which shed some light on the reaction mechanism. Following the discovery in 2006 that a linked phosphine-borane system could reversibly activate hydrogen2 a tremendous effort has been put forth to understand and expand this unprecedented reactivity.3,4 This new archetype for metal-free small molecule activation, containing a bulky Lewis acid and Lewis base which are unable to bond directly due to steric repulsion, has been termed a “frustrated Lewis pair” (FLP).3,4 The FLP concept is expanded to include bulky P-P bound species, pyridines and P-O bound Lewis bases as partners for B(C6F5)3. In some cases small molecule activation produced ion pairs or zwitterions related to those found for reactions with tertiary phosphines,3,4 but in others novel reaction pathways were discovered including phosphorus-phosphorus bond cleavage, catalytic hydrogenations and the formation of novel intramolecular FLPs. An unexpected situation was observed for the pair of 2,6-lutidine with B(C6F5)3, where adduct formation was observed along with free Lewis acid and base, but H2 activation by the FLP proceeded smoothly. Covalently bound phosphinoboranes of the general formula R2PB(C6F5)2 are synthesized. While systems with small R groups dimerized, monomers existed for cases with bulkier R groups. These monomers were found to exhibit extraordinarily short phosphorus-boron bonds yet were still capable of H2 activation analogous to bimolecular phosphine-borane systems. These systems also showed unique reactivity with Lewis acids and Lewis bases. This work further demonstrates the broad and general utility of the FLP concept in the synthesis of new materials and in catalytic transformations.

Wnt signaling is important in human development and disease, thus dysregulated beta-catenin constitutes an attractive target for drug intervention. The few functional inhibitors currently available target transcriptional activation, therefore, identifying novel upstream modulators would be of tremendous importance to elucidating the mechanisms involved in regulatingbeta-catenin activity. To achieve this, I developed a high-throughput screen to assess beta-catenin stability in mammalian cells using a luciferase tagged beta-catenin molecule. This assay was used to screen three chemical libraries to identify small molecule modulators of the pathway. Identified inhibitors/activators of the pathway were investigated via secondary assays. The most promising inhibitor, 21H7, significantly attenuated activated beta-catenin signaling in colon cancer cells, decreasing beta-catenin stability. The inhibitory effects of 21H7 and a structurally similar compound were shown to not only inhibit Wnt target gene expression in colon cancer cells, but also prostate cancer lines. Thus, 21H7 represents an attractive lead compound for further study.

Cancer accounts for nearly one-quarter of deaths in the United States, exceeded only by heart diseases. In 2006, there were 559,888 cancer deaths in the US. Finding effective treatments for cancer is a major challenge among researchers. In solid tumor, hypoxia increases the progression of malignancy and metastasis by promoting angiogenesis. The transcription factor HIF-1 is responsible for the regulation of cellular processes, including glycolysis and angiogenesis. Clinical evidence has determined that expression of HIF-1 is strongly associated with poor patient prognosis. Also, activation of HIF-1 contributes to malignant behavior and therapeutic resistance. In view of these observations, there is a need for anti-cancer treatments that addresses hypoxic related tumors. HIF-1 presents a viable target for inhibition of tumor growth with small molecules. Herein, we describe the design and synthesis of small molecules that inhibit the HIF-1 pathway, as well as mechanistic studies involved in the investigation of the mode of action of these compounds.

Wnt signaling is important in human development and disease, thus dysregulated beta-catenin constitutes an attractive target for drug intervention. The few functional inhibitors currently available target transcriptional activation, therefore, identifying novel upstream modulators would be of tremendous importance to elucidating the mechanisms involved in regulatingbeta-catenin activity. To achieve this, I developed a high-throughput screen to assess beta-catenin stability in mammalian cells using a luciferase tagged beta-catenin molecule. This assay was used to screen three chemical libraries to identify small molecule modulators of the pathway. Identified inhibitors/activators of the pathway were investigated via secondary assays. The most promising inhibitor, 21H7, significantly attenuated activated beta-catenin signaling in colon cancer cells, decreasing beta-catenin stability. The inhibitory effects of 21H7 and a structurally similar compound were shown to not only inhibit Wnt target gene expression in colon cancer cells, but also prostate cancer lines. Thus, 21H7 represents an attractive lead compound for further study.

Stoichiometric and catalytic small molecule activation reactions are vital for the synthesis of new materials. The activation of phosphorus-hydrogen or phosphorus-phosphorus bonds allows for the facile synthesis of new phosphorus-containing molecules for a wide variety of applications.1 An investigation of the P-H dehydrocoupling reaction was undertaken utilizing two rhodium(I) based catalysts. Over the course of this investigation it was found that the Rh(I) systems were also active catalysts for the reverse reaction: phosphorus-phosphorus bond hydrogenation (and hydrosilylation). This reaction was exploited for the synthesis of novel phosphines from P-P bound species. Molecules with P-P bonds were reacted in a stoichiometric fashion with the catalyst precursor, producing a variety of novel species with interesting bonding features which shed some light on the reaction mechanism. Following the discovery in 2006 that a linked phosphine-borane system could reversibly activate hydrogen2 a tremendous effort has been put forth to understand and expand this unprecedented reactivity.3,4 This new archetype for metal-free small molecule activation, containing a bulky Lewis acid and Lewis base which are unable to bond directly due to steric repulsion, has been termed a “frustrated Lewis pair” (FLP).3,4 The FLP concept is expanded to include bulky P-P bound species, pyridines and P-O bound Lewis bases as partners for B(C6F5)3. In some cases small molecule activation produced ion pairs or zwitterions related to those found for reactions with tertiary phosphines,3,4 but in others novel reaction pathways were discovered including phosphorus-phosphorus bond cleavage, catalytic hydrogenations and the formation of novel intramolecular FLPs. An unexpected situation was observed for the pair of 2,6-lutidine with B(C6F5)3, where adduct formation was observed along with free Lewis acid and base, but H2 activation by the FLP proceeded smoothly. Covalently bound phosphinoboranes of the general formula R2PB(C6F5)2 are synthesized. While systems with small R groups dimerized, monomers existed for cases with bulkier R groups. These monomers were found to exhibit extraordinarily short phosphorus-boron bonds yet were still capable of H2 activation analogous to bimolecular phosphine-borane systems. These systems also showed unique reactivity with Lewis acids and Lewis bases. This work further demonstrates the broad and general utility of the FLP concept in the synthesis of new materials and in catalytic transformations.