In this work a system-level approach was taken to the single-molecule fluorescence microscopy of living cells. This primarily involved the unification of relevant information within appropriately structured artefacts that were used to inform and enhance experimentation. Initially the diversity of emerging single-molecule techniques was reviewed and presented with a novel article structure to suit the purpose of designing an experiment (Harriman and Leake 2011). Techniques were grouped by the type of information they could access, rather than the standard organisation centred on the techniques themselves. A bespoke microscope was conceived and built with reference to knowledge and tools from the fields of Architecture and Systems-Engineering. The microscope layout would enable multiple experiment types through independent control of multiple illumination beams. A technique was developed enabling the prescription of evanescent field penetration depth for each incident beam. The various empirical and theoretical results that are used to understand and modify a microscopy experiment were integrated into an internally consistent simulation model (Harriman and Leake. 2013). This was used to inform the selection of experimental components and parameters and ultimately acquire higher data quality as measured by functions such as signal-to-noise ratio (SNR). The combined experimental system of microscope and simulation model was applied in two live-cell investigations. In Escherichia coli, the spatial distribution of membrane bound proteins was investigated and a novel technique was applied to the analysis of colocalisation. Results indicate that NADH dehydrogenase and ATP synthase follow uncorrelated trajectories. This supports the hypothesis of spatial decoupling of molecules that energise the membrane and molecules that use membrane energy. In human carcinoma cells, the mechanism of ligand-receptor binding was investigated. Data was collected prior to and periodically after the addition of ligands, and fluorescence images were acquired of both ligands and receptors. Analyses based on single particle tracking are currently being carried out by a collaborator to extract information on stoichiometry and dynamics at the single-molecule level.

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.

The repression of the E. coli lac operon seems to be more efficient than the current theoretical model allows for. Specifically, it is more quiet than expected during the replication of the chromosome. I have induced cells during short periods and counted the number of protein products from the operon to determine if there is a delay in activation of transcription that could account for the discrepancy. The results are compatible with a delay of 10-20 s, but the delay could not be conclusively proven. Furthermore, it has been investigated if the mechanism behind the delay might be differential localization of the lac operon with and without induction. It is shown that the lac operon is more often located in the periphery of the cell and in the internucleoid region when induced. These might be regions where genes are higher expressed, giving a delay in expression after de-repression before the gene is transported there.

Rotaviruses are the single most common cause of fatal and severe childhood diarrhoeal illness worldwide (>125 million cases annually). Rotavirus shares structural and functional features with many viruses, such as the presence of segmented double-stranded RNA genomes selectively and tightly packed with a conserved number of transcription complexes in icosahedral capsids. Nascent transcripts exit the capsid through 12 channels, but it is unknown whether these channels specialise in specific transcripts or simply act as general exit conduits; a detailed description of this process is needed for understanding viral replication and genomic organisation. To test these opposing models, a novel single-molecule assay was developed for the capture and identification (CID) of newly synthesised specific RNA transcripts. CID combines the hybridisation of transcripts with biotinylated and FRET compatible labelled ssDNAs with the implementation of recent developments in single molecule fluorescence such as alternating laser excitation (ALEX) and total internal reflection fluorescence (TIRF) microscopy. CID identifies and quantifies specific transcripts of rotavirus based on a FRET/Stoichiometry (E*/S) value of the hybridised labelled probes. I used CID to pull down the capsid on the surface slide and identify partially extruded transcripts of three different segments 2, 6 and 11. The findings presented in this thesis support a model in which each channel specialises in extruding transcripts of a specific segment, that in turn is linked to a single transcription complex. The method can be extended to study other transcription systems including E.coli, and can be further developed as a potential diagnostic tool.

DNA replication is a fundamental cellular process. However, the structure and dynamics of the eukaryotic DNA replication machinery remain poorly understood. A soluble extract system prepared from Xenopus eggs recapitulates eukaryotic DNA replication outside of a cell on a variety of DNA templates. This system has been used to reveal many aspects of DNA replication using a variety of ensemble biochemical techniques. Single-molecule fluorescence imaging is a powerful tool to dissect biochemical mechanisms. By immobilizing or confining a substrate, its interaction with individual, soluble, fluorescently-labeled reactants can be imaged over time and without the need for synchrony. These molecular movies reveal binding parameters of the reactant and any population heterogeneity. Moreover, if the experiments are imaged in wide-field format, the location or motion of the labeled species along the substrate can be followed with nanometer accuracy. This dissertation describes the use and development of novel single-molecule fluorescence imaging techniques to study eukaryotic DNA replication. A biophysical characterization of a replication fork protein, PCNA, revealed both helical and non-helical sliding modes along DNA. Previous experiments demonstrate that the egg extracts efficiently replicate surface-immobilized linear DNA. This finding suggested replication of DNA could be followed as motion of the replication fork along the extended DNA. However, individual proteins bound at the replication fork could not be visualized in the wide-field due to the background from the high concentration of the fluorescent protein needed to compete with the extract’s endogenous protein. To overcome this concentration barrier, I have developed a wide-field technique that enables sensitive detection of single molecules at micromolar concentrations of the labeled protein of interest. The acronym for this method, PhADE, denotes three essential steps: (1) Localized PhotoActivation of fluorescence at the immobilized substrate, (2) Diffusion of unbound fluorescent molecules to reduce the background and (3) Excitation and imaging of the substrate-bound molecules. PhADE imaging of flap endonuclease I (Fen1) during replication revealed the time-evolved pattern of replication initiation, elongation and termination and the kinetics of Fen1 exchange during Okazaki fragment maturation. In the future, PhADE will enable the elucidation of the dynamic events at the eukaryotic DNA replication fork. PhADE will also be broadly applicable to the investigation of other complex biochemical process and low affinity interactions. It will be especially useful to those researchers wishing to correlate motion with binding events.

Doctor of Philosophy / Department of Chemical Engineering / Keith L. Hohn / Amorphous silica-alumina is widely used as a solid acid catalyst for various reactions in oil refining and the petrochemical industry. The strength and the number of the acid sites in the material are most often believed to arise from the alumina atoms inserted into the silica lattice. The existence of the acidity distribution across the framework is a result of the local composition or the short-range interactions on the silica-alumina surface. Conventional techniques used to characterize silica-alumina provide effective information on the average acidity, but may not reflect the heterogeneity of surface acidity within the material. Recently, it is possible to study individual catalytic sites on solid catalysts by single molecule fluorescence microscopy with high time and space resolution. Fluorophores can be chosen that emit at different wavelengths depending on the properties of the local environment. By doping these fluorophores into a solid matrix at nanomolar concentrations, individual probe molecules can be imaged. Valuable information can be extracted by analyzing changes in the fluorescence spectrum of the guest molecules within a host matrix. In this research, silica-alumina thin films were studied with single molecule fluorescence microscopy. The samples were prepared by a sol-gel method and a wide-field fluorescence microscope was used to locate and characterize the fluorescent behaviors of pH sensitive probes. In mesoporous thin films, the ratio of the dye emission at two wavelengths provides an effective means to sense the effective pH of the microenvironment in which each molecule resides. The goal of this work was to develop methods to quantify the acidity of individual micro-environments in heterogeneous networks. Pure silica films treated with external phosphate solutions of different pH values were used to provide references of the fluorescence signals from individual dye molecules. SM emission data were obtained from mesoporous Al-Si films as a function of Al content in films ranging from 0% to 20% alumina. Histograms of the emission ratio revealed that films became more acidic with increasing Al content. The acidity on interior surfaces in zeolite pores was also of interest in this work. A microfluidic device was built to isolate the interior surface from the exterior surface. Some preliminary results showed the potential of using SM fluorescence method to study the acidic properties inside the pores of zeolite crystals.

Prions are infectious agents that cause fatal neurodegenerative diseases in the brain. The wide-accepted protein-only hypothesis states that the misfolded form of prion protein (PrP) is the sole constituent of prions, and the self-propagating process of PrP is considered to play a central role in prion pathogenesis. Prions are believed to propagate when a PrP assembly enters a cell and replicates to produce two or more fibrils, leading to an exponential increase in PrP aggregate number with time. However, the molecular basis of this process has not yet been established in detail. This prion-like replication is also suggested to be the mechanism in the development of other notorious neurodegenerative disorders, such as Alzheimer's and Parkinson's disease. In this thesis, I use single-aggregate imaging to study fibril fragmentation and elongation of individual murine PrP aggregates from seeded aggregation in vitro. From fluorescence imaging of individual PrP aggregates on the coverslip surface, elongation and fragmentation of the PrP assemblies have been directly observed. PrP elongation occurs via a structural conversion from a proteinase K (PK)-sensitive to PK-resistant conformer. Fibril fragmentation was found to be length-dependent and resulted in the formation of PK-sensitive fragments. To gain more insights into the mechanism of the spread of PrP, the quantified kinetic profiles allows the determination of the rate constants for these processes through the use of kinetic modelling. This enables the estimation of a simple framework for aggregate propagation through the brain, assuming that doubling of the aggregate number is rate-limiting. In contrast, the same method was applied to measurement for α-Synuclein (αS) aggregation, which has been suggested to be prion-like and is associated with Parkinson's disease. While αS aggregated by the same mechanism, it showed significantly slower elongation and fragmentation rate constants than PrP, leading to much slower replication rate. Furthermore, the measurements in αS aggregation has been extended to the cellular environment, I use super-resolution imaging to study the amplification of endogenous αS aggregation in cells and the transcellular spread of αS. Endogenous αS showed a clear amplification in number of aggregates with time after seed transduction, and the newly-formed αS aggregates are likely to spread through cell-to-cell transmission. The proteasome was demonstrated to possess a novel disaggregase function for αS fibrils and thus produce more seeds for further replication. It partially explains that αS aggregation in cells was found to replicate at a substantially faster rate than that in vitro. Determining the nature of the oligomers formed during aggregation has been experimentally difficult due to the lack of suitable methods capable of detecting and characterising the low level of oligomers. To address this problem, I have studied the early formation of PrP oligomers formed during aggregation in vitro using various single-molecule methods. The early aggregation of PrP is observed to form a thioflavin T (ThT)-inactive and two ThT-active species of oligomers, which differ in size and temporal evolution. The ThT-active oligomers undergo a structural conversion from a PK-sensitive to PK-resistant conformer, while a fraction of which grow into mature fibrils. These results also enable the establishment of a kinetic framework for elucidating temporal evolution of PrP aggregation and the relationship between oligomers and fibrils. Overall, my research identifies fibril elongation with fragmentation are the key molecular processes leading to PrP and αS aggregate replication, an important concept in prion biology, and provides a simple framework to estimate the rate of prion and prion-like spreading in animals. The results also show that a diverse range of oligomers is formed and co-exist during PrP aggregation which differ both in their structure and properties and provides mechanistic insights into a prion aggregation. The work provides a new quantitative approach to describe the prion-like property in neurodegenerative diseases from a kinetic perspective that can be verified in extending studies in other proteins or in cells.

Molecular motor proteins are responsible for the long range transport of vesicles and organelles inside living cells. A small number of motor types transport thousands of distinct cargoes to various regions in the cell at the same time. This requires that intracellular transport be tightly regulated, yet the details of how motor regulators and cofactors tune motor function remain unknown in most cases. In-vitro studies at the single motor level have been instrumental in understanding the function of individual motors. In this thesis work I developed the methodology to extend in-vitro experiments to interrogate motor regulation at the single molecule level. I describe my modifications to the microscope setup as well as the acquisition cycle that made this possible. By combining differential interference contrast microscopy with single molecule fluorescence imaging and optical trapping I was able to manipulate and image the cargo while imaging a fluorescently-labeled regulator binding at the site of the motors. I used lipid droplets purified from Drosophila embryos as cargoes. Lipid droplets are carried by the opposite polarity microtubule motors kinesin and dynein in the embryos, and bind specifically to microtubules in-vitro. In the presence of ATP they exhibit long-range and short-range motility. For this proof-of-principle experiment I used fluorescently labeled AMPPNP, a non-hydrolysable analogue of ATP which binds to the motor domain of kinesin when microtubule-bound, to image the binding of the nucleotide to the motor and demonstrate the activity of the motors. While a large fraction of microtubule-bound droplets co-localized with a fluorescent AMPPNP molecule, non-specific binding of the nucleotide to the microscope slide surface prevented confirming the specificity of the colocalization events. Nevertheless, these data demonstrate the ability of the methodology to capture, in real time, the process of a regulator binding the motor at the single molecule level. / text

We applied single-molecule fluorescence (SMF) methods to probe the properties of individual fluorescent probes, and to characterize the proteins of interest to which these probes were attached. One remarkable advantage of SMF spectroscopy is the ability to investigate heterogeneous subpopulations of the ensemble, which are buried in ensemble averaging in other measurements. Other advantages include the ability to probe the entire dynamic sequences of a single molecule transitioning between different conformational states. For the purpose of having an extended observation of single molecules, while maintaining the native nanoscale surroundings, we developed an improved vesicle preparation method for encapsulating scarce biological samples. SMF investigations revealed that molecules trapped in vesicles exhibit nearly ideal single-emitter behavior, which therefore recommends the vesicle encapsulation for reproducible and reliable SMF studies. Hyperactive Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein contributes significantly to human cancers, such as leukemia and lymphoma. We have proposed a novel therapeutic strategy by designing a cholesterol-based protein membrane anchor (PMA), to tether STAT3 to the cell membrane and thus inhibit unwanted transcription at the cell nucleus. We designed in vitro proof-of-concept experiments by encapsulating STAT3 and PMAs in phospholipid vesicles. The efficiency and the stability of STAT3 anchoring in the lipid membrane were interrogated via quantitative fluorescence imaging and multiparameter SMF spectroscopy. Our in vitro data paved the way for the in vivo demonstration of STAT3 inhibition in live cells, thus demonstrating that PMA-induced protein localization is a conceptually viable therapeutic strategy. The recent discovery of intrinsically disordered proteins (IDPs) highlights important exceptions to the traditional structure-function paradigm. SMF methods are very suited for probing the properties of such highly heterogeneous systems. We studied in detail the effects of electrostatics on the conformational disorder of an IDP protein, Sic1 from yeast, and found that the electrostatic repulsion is a major factor controlling the dimensions of Sic1. Based on our data we also conclude that a rod-like shape seems a better candidate than a random Gaussian chain to describe and predict the behavior of Sic1.