Single molecule studies of enzymes have revealed that nominally identical individual enzyme molecules are functionally heterogeneous. Different individual molecules exhibit different catalytic rates under identical conditions, and individual enzyme molecules show fluctuating rates over broad timescales. The structural basis and the biological sources for such heterogeneity remains poorly understood. Herein, studies are presented of the β-galactosidase from Escherichia coli, using capillary electrophoresis with laser-induced fluorescence (CE-LIF), to investigate the sources of catalytic heterogeneity at the single molecule level. Limited proteolysis as a possible source for single molecule heterogeneity, and for the changes in activity of a population of individual molecules over time, was investigated by inducing enzyme expression in two E.coli strains in the presence of a broad spectrum of protease inhibitors. The effect of protease inhibitors was found to be limited. β-Galactosidase was expressed from a lacZ linear template from two different E. coli strains using an in vitro protein expression system to determine if in vitro synthesized enzyme was identical to its in vivo counterpart. In vitro synthesized enzyme was found to be less active than in vivo sources. The differences were attributed to deficient N-terminal methionine removal and the higher rates of translation error associated with in vitro protein synthesis. Single molecule separations revealed that individual molecules of β-galactosidase were electrophoretically distinct, and that the electrophoretic heterogeneity was independent of source of enzyme, method of measurement, or of capillary coating. Electrophoretic modeling indicated that slight variation of hydrodynamic radius is the most likely source of electrophoretic mobility heterogeneity. The extent of single molecule catalytic variation was reduced in a mutant with a hyperaccurate translation phenotype implying that translation error is a source of the heterogeneity. Streptomycin-induced translation error reduced average activity, but did not lead to an increase in catalytic heterogeneity. No relationship between translation error and electrophoretic heterogeneity was observed. A novel CE-LIF assay was developed for the continuous monitoring of the catalytic activity and electrophoretic mobility of individual β-galactosidase molecules. Thermally-induced catalytic fluctuations were observed suggesting that individual enzyme molecules were capable of conformational fluctuations that supported different catalytic rates.

Over the past decade, solid-state nanopores have emerged as a versatile tool for the detection and characterization of single molecules, showing great promise in the field of personalized medicine as diagnostic and genotyping platforms. While solid-state nanopores offer increased durability and functionality over a wider range of experimental conditions compared to their biological counterparts, reliable fabrication of low-noise solid-state nanopores remains a challenge. In this thesis, a methodology for treating nanopores using high electric fields in an automated fashion by applying short (0.1-2 s) pulses of 6-10 V is presented which drastically improves the yield of nanopores that can be used for molecular recognition studies. In particular, this technique allows for sub-nanometer control over nanopore size under experimental conditions, facilitates complete wetting of nanopores, reduces noise by up to three orders of magnitude and rejuvenates used pores for further experimentation. This improvement in fabrication yield (over 90%) ultimately makes nanopore-based sensing more efficient, cost-effective and accessible. Tuning size using high electric fields facilitates nanopore fabrication and improves functionality for single-molecule experiments. Here, the use of nanopores for the detection of DNA-protein complexes is examined. As proof-of-concept, neutravidin bound to double-stranded DNA is used as a model complex. The creation of the DNA-neutravidin complex using polymerase chain reaction with biotinylated primers and subsequent purification and multiplex creation is discussed. Finally, an outlook for extending this scheme for the identification of proteins in a sample based on translocation signatures is presented which could be implemented in a portable lab-on-a-chip device for the rapid detection of disease biomarkers.

Cytoplasmic dynein is a ubiquitous minus-end directed motor protein that is essential for a variety of cellular processes ranging from cargo transport to spindle and chromosome positioning. Specifically, in fission yeast during meiotic prophase, the fused nucleus follows the spindle pole body in oscillatory movements from one cell pole to the other. The three molecular players that are essential to this process are: (i) the motor protein dynein, which powers the movement of the nucleus, (ii) microtubules, which provide the tracts for the movement and (iii) Num1, the anchor protein of dynein at the cortex. Dyneins that are localized to the anchor protein at the cortex and simultaneously bound to the microtubule emanating from the spindle pole body, pull on that microtubule leading to the movement of the nucleus. The spindle pole body, by virtue of its movement establishes a leading and a trailing side. Previous work by Vogel et al. has elucidated the mechanism of these oscillations as that of asymmetric distribution of dynein between the leading and trailing sides. This differential distribution is a result of the load-dependent detachment of dynein preferentially from the trailing microtubules. This self-organization model for dynein, however, requires a continuous redistribution of dynein from the trailing to the leading side. In addition, dyneins need to be bound to the anchor protein to be able to produce force on the microtubules. Anchored dyneins are responsible for many other important processes in the cell such as spindle alignment and orientation, spindle separation and rotation. So we set out to elucidate the mechanism of redistribution of dynein as well as the targeting mechanism of dynein from the cytoplasm to cortical anchoring sites where they can produce pulling force on microtubules. By employing single-molecule observation using highly inclined laminated optical sheet (HILO) microscopy and tracking of fluorescently-tagged dyneins using a custom software, we were able to show that dyneins redistributed in the cytoplasm of fission yeast by simple diffusion. We also observed that dynein bound first to the microtubule and not directly to the anchor protein Num1. In addition, we were able to capture unbinding events of single dyneins from the microtubule to the cytoplasm. Surprisingly, dynein bound to the microtubule exhibited diffusive behaviour. The switch from diffusive to directed movement required to power nuclear oscillations occurred when dynein bound to its cortical anchor Num1. In summary, dynein employs a two-step targeting mechanism from the cytoplasm to the cortical anchoring sites, with the attachment to the microtubule acting as the intermediate step.

Theileria parva is a complex protozoan parasite causing East Coast fever in Eastern and Central Africa. Vaccination using live parasites is an effective control measure and has been used in Zambia based on locally isolated and introduced T. parva stocks. Diversity among T. parva populations was investigated in parasites from two Zambian provinces with different disease epidemiologies and control histories. Isolates from the pre-vaccination era, local and exotic stocks used for vaccination, and one recent field isolate were cloned and passaged in vitro to study genomic stability over time. The results of the data from three genome-wide probes indicate a marked homogeneity and stability among the Zambian isolates in contrast to East African isolates. Results from Southern blot profiles and the polymorphic immunodominant molecule (PIM) sequence analysis suggest a common origin for the Zambian isolates from the pre-vaccination era, except for one isolate (Zam5) from Southern Province. This isolate showed characteristics suggesting a buffalo origin. Assays for genotype characterisation were developed using five allelic markers. Multilocus characterisation revealed identical profiles in a recent Zambian isolate from Southern Province and two components of an exotic cocktail vaccine, indicating the escape of one of the vaccine stocks in the field. Characterisation of T. parva field populations by RFLP-PCR assays after immunisation revealed the presence of dominant genotypes from those that had been used for vaccination. Circumstantial evidence for the involvement of one of the exotic vaccine parasites in epidemics in Southern Province is presented and a hypothesis formulated for the rapid spread of this genotype. Analysis of the characterisation data suggested the existence of two groups of T. parva parasites of different origin. The classic T. parva group, characterised by a dimorphism of the p150, p104 and p32 loci and the absence of a p67 insert and a buffalo-derived group which showed a polymorphism of p150, p104 and p32 and the presence of a p67 insert. There is evidence that recombination occurs, resulting in parasites that have characteristics of both groups. The relevance of these recombinant parasites in the epidemiology of the disease seems low. Characterisation of larger samples from areas of regular buffalo-cattle contact is necessary to clarify this. Sequence analysis of the most discriminative locus (PIM) was undertaken and gene conversion could be the main mechanism generating diversity. A more appropriate nomenclature for T. parva is proposed based on the growing evidence of molecular differences among isolates and stocks.

A simple theory relating the dynamics of electrons to the long-range properties of the molecular ionic core is developed for asymmetric top molecules in general and water in particular. It is combined with the molecular version of multichannel quantum defect theory developed by Fano and Jungen and applied to the resonance-enhanced multiphoton ionization spectra of Child and Glab (M. S. Child and W. G. Glab, J. Chem. Phys., 2001, 112, 3754-3765), the mass-analysed threshold ionization spectra of Dickinson et al. (H. Dickinson, S. R. Mackenzie and T. P. Softley, Phys. Chem. Chem. Phys., 2000, 2, 4669-4675) and the as-yet unpublished work of Glab on the photoelectron branching ratios of the nd and nf Rydberg lines of the water molecule. The effect of resonances between electronic and rotational motion in Rydberg molecules is investigated using multichannel quantum defect theory with special reference to the time-resolved wave packet experiments of Smith et al. (R. A. L. Smith, J. R. R. Verlet, E. D. Boleat, V. G. Stavros and H. H. Fielding, Faraday Discuss., 2000, 115, 63-70).

Bacterial cells reproduce by doubling in size and dividing. The molecular control systems which regulate the cell cycle must do so in a manner which maintains a similar cell size over many generations. A cell can under conditions of fast growth conclude cell cycles in shorter time than the time required to replicate its chromosome. Under such conditions several rounds of replication are maintained in parallel and a cell will inherit replication processes which were initiated by an ancestor. To accomplish this the cell has to initiate and terminate one round of replication during each cell cycle. To investigate the effects of the cell cycle on gene-regulation in the gut bacterium Escherichia coli, an experimental method combining microfluidics, single molecule fluorescence microscopy and automated analysis capable of acquiring an arbitrary number of complete cell cycles per experiment was developed. The method allowed for the rapid exchange of the chemical environment surrounding the cells. Using this method it was possible to measure the dissociation time of the transcription factor molecule, LacI-Venus, from the native lactose operator sequence, lacO1, and an artificially strong operator, lacOsym, in vivo. The results indicated that regulation of gene-expression from the lactose operon does not occur at equilibrium in living cells. Furthermore, by studying the intracellular location of non-specifically interacting transcription factor molecules it was possible to determine that these do not form long-lived gradients inside the cell as was previously proposed. By studying the replication machinery and the origin of replication it was found that replication is initiated according to a cell volume per origin which did not vary over different growth conditions. Further, division timing was found to be determined by the initiation event to occur after a fixed time-delay. A consequence of this mode of regulation is an uncertainty relation between the size at birth and the cell cycle time, in which cells will vary more in in the cycle time during conditions of slow growth as compared to fast growth and vary more in birth length during conditions of fast growth as compared to slow growth.

While hundreds of papers have been published on frustrated Lewis pairs (FLPs) – the combination of bulky Lewis acids and bases which cannot form adducts – few of these use aluminum-based Lewis acids. The research outlined in this thesis expands the small molecule activation chemistry of FLPs to include Al.Combinations of bulky phosphines and AlX3 (X = halide or C6F5) with CO2 leads to the rapid activation to form the complexes R3P(CO2)(AlX3)2 (R = otol, Mes). Subsequent treatment with ammonia borane (AB) results in the rapid reduction of the CO2 fragment to methanol after water quench. Subsequent reactivity studies have established that AB adducts of AlX3, which react with CO2, are key intermediates in this chemistry. Further studies with Mes3P(CO2)(AlX3)2 revealed that these can reduce exogenous CO2 to CO, along with the generation of Mes3P(C(OAlX2)2O)(AlX3) and [Mes3PX][AlX4]. Detailed experimental and theoretical mechanistic investigations outline a possible mechanism involving direct CO2 insertion into free AlX3, followed by nucleophilic attack by PMes3 resulting in the expulsion of CO. Reactions with olefins were also investigated. While addition products of the type R3P(CH2CH2)AlX3 could be obtained with ethylene, C–H bond activation occurred with bulkier olefins. The resulting allyl species underwent subsequent C–C bond forming reactions with other olefins or CO2. Hydrogen was also activated using PR3/AlX3 FLPs to form species of the general formula, [R3PH][(H)(AlX3)2] (X = I, C6F5). These were found to reduce unactivated olefins, generating the redistributed products [R3PH][AlX4] and RAlX2 (R = alkyl). Attempts to circumvent this redistribution and favour alkyl protonation, thus generating a catalytic hydrogenation catalyst, are also discussed. Finally, the activation of N2O was also examined. While addition products could be formed, unexpected aromatic or benzylic C–H bond activation chemistry occurred in the presence of excess Al. A radical reaction pathway is proposed

Three classes of bifunctional compounds related to frustrated Lewis pair chemistry were studied. The first class, alkynyl-linked phosphonium borates, was strategically synthesized and the corresponding neutral alkynyl-linked phosphine boranes generated in solution. They were reacted with THF, alkenes and alkynes to undergo either ring-opening or multiple bond addition reactions, giving rise to zwitterionic macrocycles. In two select alkynyl-linked phosphonium borates, thermolysis resulted in unique rearrangements transforming the phosphino- and boryl-substituted alkynyl moieties into C4 chains. The alkynyl-linked phosphine boranes were further demonstrated to coordinate as η3-BCC ligands in Ni(0) complexes. The rigid nature of the coordination was confirmed by dimerization without cleavage of the Ni–B interaction upon the addition of acetonitrile or carbon monoxide. Moreover, reactions with Al-, Zn- and B-based Lewis acids prompted hydride transfer within the alkynyl-linked phosphonium borate and interesting functional group transfer reactions. The second class of the bifunctional systems, a series of gem-substituted bis-boranes, was subjected to reactions with tBu3P and CO2. The O-linked bis-borane was shown to coordinate the phosphino-carboxylate moiety with one B, while the methylene-linked bis-boranes were demonstrated to chelate the carboxyl group. The third bifunctional system class, vinyl-group tethered boranes, was examined to elucidate the mechanism of the frustrated Lewis pair addition reaction to olefins. Using a bis(pentafluorophenyl)alkylborane, the close proximity of the olefinic protons and the ortho-fluorine nuclei were evident by both NOE measurements and DFT calculations. Moreover, its reactions with phosphine bases suggested that an initial interaction between the highly electrophilic borane and the olefinic fragment precedes such frustrated Lewis pair addition reaction. Furthermore, a bis(pentafluorophenyl)alkoxyborane was synthesized and reacted with P-, N-, C- and H-based nucleophiles, demonstrating the wide range of Lewis bases that can be applied in olefin addition reactions with complementary regioselectivity.

While hundreds of papers have been published on frustrated Lewis pairs (FLPs) – the combination of bulky Lewis acids and bases which cannot form adducts – few of these use aluminum-based Lewis acids. The research outlined in this thesis expands the small molecule activation chemistry of FLPs to include Al.Combinations of bulky phosphines and AlX3 (X = halide or C6F5) with CO2 leads to the rapid activation to form the complexes R3P(CO2)(AlX3)2 (R = otol, Mes). Subsequent treatment with ammonia borane (AB) results in the rapid reduction of the CO2 fragment to methanol after water quench. Subsequent reactivity studies have established that AB adducts of AlX3, which react with CO2, are key intermediates in this chemistry. Further studies with Mes3P(CO2)(AlX3)2 revealed that these can reduce exogenous CO2 to CO, along with the generation of Mes3P(C(OAlX2)2O)(AlX3) and [Mes3PX][AlX4]. Detailed experimental and theoretical mechanistic investigations outline a possible mechanism involving direct CO2 insertion into free AlX3, followed by nucleophilic attack by PMes3 resulting in the expulsion of CO. Reactions with olefins were also investigated. While addition products of the type R3P(CH2CH2)AlX3 could be obtained with ethylene, C–H bond activation occurred with bulkier olefins. The resulting allyl species underwent subsequent C–C bond forming reactions with other olefins or CO2. Hydrogen was also activated using PR3/AlX3 FLPs to form species of the general formula, [R3PH][(H)(AlX3)2] (X = I, C6F5). These were found to reduce unactivated olefins, generating the redistributed products [R3PH][AlX4] and RAlX2 (R = alkyl). Attempts to circumvent this redistribution and favour alkyl protonation, thus generating a catalytic hydrogenation catalyst, are also discussed. Finally, the activation of N2O was also examined. While addition products could be formed, unexpected aromatic or benzylic C–H bond activation chemistry occurred in the presence of excess Al. A radical reaction pathway is proposed

One of the largest problems in current medicine is the shortage of organs for transplant due to technological limitations in the storage of organs for any length of time. A possible solution to this problem would involve cryopreservation. However, current cryopreservatives such as sucrose or DMSO have concerning cytotoxic issues that limit their possible applications. A major cause of cryoinjury is the uncontrolled recrystallization of inter and intra-cellular ice crystals that occurs during the thawing process leading to mechanical damage and dehydration. The Ben lab has thus been interested in the design of compounds that are capable of inhibiting this process but do not possess other undesirable properties found in the native compounds. These synthetic analogues have been shown to increase cellular viability post-thaw. A series of mixed α/β glycopeptides are prepared and analyzed for antifreeze properties. The results of this study imply that it is not the gross conformation of the glycopeptide that is responsible for activity, but rather that intramolecular relationships may be responsible for disrupting the reorganization of ice. A technique was devised for the incorporation of triazoles into the analogues to investigate the importance of the linker and to greatly simplify the synthesis of a library of glycoconjugates. It was found that the IRI activity of glycopeptides is very sensitive to the distance between carbohydrate and peptide backbone. The electron density at the anomeric oxygen is an important parameter with respect to intramolecular networks. A series of substituted galactosides is presented that modify the electronics of the anomeric oxygen. The results demonstrate that decreasing electron density at this position appears to improve IRI activity in a predictable manner. To better understand the remarkable IRI activity of a key analogue, it was systematically truncated. This study led to the serendipitous discovery of a series of very highly IRI active analogues that do not contain a peptide backbone. These compounds represent the first non-glycopeptides that can show very significant IRI activity even at very low concentrations. The final portion of the thesis reports the efforts towards the preparation of a carbasugar analogue of AFGP-8.