Hybrid trap experiments are set-ups that allow to study the interaction between ions and atoms in cold controlled environment. In such context, molecular anions present specific theoretical and experimental interests and challenges. In this work, we have used extensive \textit{ab initio} methods to investigate several collisional anionic systems: (1) M + OH$^{-}$ (where M are alkali or alkaline earth atoms), (2) Rb and H + OH(H$_{2}$O)$_{n}^{-}$ (with $n=0,1,2,3,4$) and (3) Rb and Li + C$_{2}^{-}$. Several molecular properties such as vertical detachment energies or electroaffinities, optimized structures, harmonic frequencies, potential energy curves or surfaces, etc have been calculated using high level quantum chemistry approaches. The results have been used to make predictions on the related reactivity in low energy regime. We emphasis on electronic detachment processes by carefully analysing the difference between the neutral and anionic potential energy surface. The Rb + OH$^{-}$ system is currently under experimental investigation. Therefore, a detailed study of its reactivity is carried out in the present work. We have analysed the different reactive channels arising from both collision involving the ground state and first electronic excited state of Rb. Using our calculated potentials and a capture model based dynamics, we have extracted cross sections and rate constants. Comparison with other alkali and earth alkaline atoms are made. Hydrated hydroxide cluster anions are planned by the experimental group as upcoming studied systems. We present here our preliminary results on the possible outcome when considering collisions with Rb and we discuss their implications for hybrid trap experiments. We make comparison with H as a colliding partner and consider our results in the context of astrochemistry. Finally we propose the C$_{2}^{-}$ molecular anion as an alternative to OH$^{-}$. Its interaction and reactivity with Rb and Li are investigated and the results are used to motivate our suggestion. Furthermore, for the Rb+OH$^{-}$ and Rb+C$_{2}^{-}$ system, we have also investigated the effect of a non-thermal collision energy distribution on the rate constants. At last, in light of the discussions related to each topic, general conclusions on the use of molecular anions in hybrid trap experiments are drawn. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

La synthèse des protéines est un mécanisme central de la vie cellulaire dont la compréhension est un enjeu du domaine biomédical. Les études en molécule unique permettent d’observer chaque système réactionnel individuellement et donnent accès à des évènements asynchrones difficilement observables en mesure d’ensemble, tels la traduction de protéines.Cette thèse présente les premiers résultats en molécule unique sur la traduction par un ribosome eucaryote (mammifère). Nous observons les systèmes traductionnels grâce à des marqueurs fluorescents liés à des oligonucléotides pouvant s’hybrider sur les séquences d’ARN traduites. L’observation de ces marqueurs est faite par microscopie de fluorescence en onde évanescente (TIRF), les ARN étant fixés sur une lamelle de microscope. En lisant l’ARN, le ribosome détache les marqueurs, et leurs instants de départs donnent des informations sur le passage du ribosome à différentes positions sur l’ARN. Cette méthode permet d’obtenir des données cinétiques sur un grand nombre de systèmes traductionnels en parallèle pouvant alors être interpolées par des lois de probabilité. Nous obtenons par cette méthode des mesures de la cinétique in vitro de l’élongation eucaryote et nous observons un délai dû à une initiation non-canonique. En effet, nous complexons le ribosome sur l’ARN grâce à une structure de type IRES. Dans nos conditions d’expérience, l’incorporation d’un acide aminé prend environ une seconde tandis que cette structure induit un retard à la traduction de plusieurs dizaines de secondes. Ces résultats ouvrent des perspectives d’étude cinétique dans des cas plus complexes tels le franchissement de structures secondaires de l’ARN. / Protein synthesis is a central mechanism of cellular life and understanding it is a challenge in biomedical research. Single molecule studies permit each reactive system to be observed individually and provide access to asynchronous events difficult to observe in ensemble experiments, such as protein translation.This thesis presents the first results on single molecule eukaryotic (mammalian) translation. We observe the translational systems using fluorophores linked to oligonucleotides annealed to the RNA translated sequences. The observation of these fluorophores is done by total internal reflection fluorescence microscopy, the RNA being attached to a microscope slide. When reading the RNA, the ribosome unzips the fluorescent oligonucleotides and their departure times provide information about the position of the ribosome at different locations on the RNA strand. This method provides kinetic data on a large number of parallel translational systems that can be fitted using probability laws.With this method, we measure the in vitro kinetics of eukaryotic elongation and we reveal a delay due to a non-canonical initiation of the ribosome. Indeed, in our experiments, the ribosome is initially complexed on an RNA structure called Internal Ribosome Entry Site. In our experimental conditions, each incorporation of an amino acid in the nascent protein takes about one second while the IRES structure induces a delay of several tens of seconds on the first incorporation. These results open new perspectives for kinetic studies in more complex configurations such as the passage of the ribosome through RNA secondary structures.

A técnica de ressonância ciclotrônica de íons permite aprisionar numa cela adequada íons produzidos por impacto de elétrons sobre um gás a baixa pressão (10-7 - 10-4 Torr) . Os íons são mantidos na cela por tempos de 3 a 10 ms e dessa maneira podem reagir com moléculas neutras do gás do qual provém ou, de algum outro gás introduzido no espectrômetro. Resultam dessas reações produtos iônicos, que frequentemente foram observados reagirem novamente com moléculas neutras, dando origem a íons terciários. Todos os íons são detectados pela potência que absorvem de um campo de rádio-frequência conveniente, podendo ser registrado um espectro, no qual cada íon é caracterizado por sua massa, sendo a intensidade do pico correspondente proporcional à corrente iônica parcial do lon na cela. Contudo, a situação é tal que íons de massa maior permanecem por tempos mais longos na cela, de modo a reagirem em maior extensão e absorverem maior potência do oscilador de rádio-frequência. Essa discriminação de massa precisa ser levada em conta ao interpretar os espectros de ressonância ciclotrônica de íons e, para esclarecer a natureza das correções necessárias, as principais equações que descrevem o movimento dos íons na cela foram deduzidas e discutidas na primeira parte deste trabalho. Tais equações sugerem urna série de experiências, que tornam a espectroscopia de ressonância ciclotrônica de íons uma técnica muito versátil. Estas experiências foram todas apresentadas na primeira parte, devendo-se salientar a experiência de ressonância dupla, que permite identificar de maneira inequívoca o precursor de algum produto iônico, a experiência de ejeção de íons, que permite remover seletivamente um íon de dada espécie da cela, além de experiências que visam a obtenção de constantes de velocidade de reações de íons com moléculas. É justamente esta última grandeza mencionada, a saber, a constante de velocidade de uma reação, a que pode ser com parada com valores calculados a partir de modelos teóricos. Esses modelos baseiam-se em sua maioria na interação do íon, considerado como carga puntiforme, com a molécula neutra de certa polarizabilidade e momento dipolar (modelo de polarização) ou, na fragmentação de um complexo intermediário (modelos estatísticos). Os aspectos teóricos das reações entre íons e moléculas em fase gasosa foram analisados e os modelos mencionados, discutidos, além de modelos chamados \"diretos\" mais apropriados para comparações com resultados de experiências de feixes iônicos. A espectroscopia de ressonância ciclotrônica de íons foi utilizada para o estudo de reações de acilação em cetonas, reações bastante gerais (foi verificado que ocorrem também em outros sistemas carbonílicos) e que podem ser representadas pela equação RCOR\'+ + RCOR\' &#8594; RCO+ (RCOR\') + R\'. Estudos de variação das correntes iônicas relativas de todos os íons das cetonas, em função da pressão de cetona neutra, possibitaram a dedução de um mecanismo de formação desses íons acilados. Os resultados estão de acordo com um esquema no qual esse produto é formado pela fragmentação de um dímero intermediário, para o qual se supõe existirem condições de estado estacionário. Esta fragmentação se dá de maneira análoga à fragmentação dos íons moleculares de cetonas em espectroscopia de massa usual, tratando-se então de uma fragmentação induzida por uma espécie neutra. A pressões elevadas, nas quais o dímero pode sofrer colisões não-reativas e relaxar o excesso de energia interna, o mesmo é estabilizado, fornecendo um pico no espectro. Cetonas de polarizabilidade maior têm uma afinidade maior para o grupo acila; isto foi concluído, quando foram observadas reações de transferência de grupos acila, como por exemplo a transferência de CH3CO+ da cetona para a butanona num sistema formado pela mistura dessas duas cetonas. Estudos de basicidade relativa de álcoois, ácidos, ésteres e cetonas revelaram que há uma relação de proporcionalidade entre a basicidade desses compostos e seu potencial de ionização. Isto havia sido mostrado anteriormente para o caso das aminas, por outros pesquisadores. O conhecimento da basicidade de álcoois, ácidos e ésteres permitiu analisar reações de esterificação e transesterificação sob o ponto de vista termoquímico. Trata-se de reações entre moléculas protonadas das espécies mencionadas, que podem ser consideradas análogas às reações catalisadas por ácidos em solução. O fato de uma reação ser exotérmica não significa que ela ocorra. Assim, foi observado que ácido fórmico não é esterificado por metanol ou etanol nas condições reinantes numa cela de ressonância ciclotrônica de íons, enquanto quê ácido acético o é. A ordem relativa de basicidades em fase gasosa foi determinada como sendo HCOOH < ( CH30H < C2H5OH < CH3COOH. Dessa maneira os resultados estão de acordo com um ataque nucleófilo por parte do álcool no ácido protonado; porém, se este é menos básico que o álcool, ocorre a transferência de próton e não a esterificação. Reações de transesterificação não foram observadas de maneira alguma, mas uma outra reação entre ésteres e álcoois foi encontrada e que pode ser exemplificada pela equação (CH3)2CHOH2+ + HCOOC3H7 &#8594; HCO2(C3H7) (C3H7)+ + H2O. Esta reação só se dá com álcoois capazes de produzir íons de carbônio mais estáveis que os primários; portanto metanol e etanol não reagem. O produto formado pode fragmentar novamente O que revelou que o grupo alquila proveniente do álcool retém um excesso de energia na sua ligação, pois na decomposição é esta a ligação que rompe. Em todos estes estudos, isto é, nos de acilação de cetonas e de esterificação, bem como nos estudos de basicidade, foi sempre salientada a importância de examinar essas reações em fase gasosa, pelo fato de serem reações mais simples, uma vez que se dão na ausência de solventes e portanto revelarem propriedades intrínsecas das espécies envolvidas. Finalmente foram descritas algumas modificações realizadas no espectrômetro de ressonância ciclotrônica de íons, para poder operá-lo de forma pulsada. Com isso é possível manter os íons por tempos maiores na cela (500 ms) e, o que é mais importante, esses tempos podem ser definidos com grande precisão, o que torna viável a obtenção de resultados quantitativos (constantes de velocidade de reação) melhores. / Ions can be trapped for times as long as 10 ms by the combined action of magnetic and electric fields in the cell of an ion cyclotron resonance spectrometer. Despite the low operating pressure (10-7 - 10-4 Torr), the ions experience many collisions during this time, some of which may be reactive, leading to product ions. The ion cyclotron resonance spectrum thus displays a series of peaks corresponding to the various primary, secondary, and eventually tertiary ions; the peak heights, after suitable mass correction, yield ion currents. The double resonance technique allows one to establish unambiguously the precursor ions of a given product ion, by accelerating the suspected reagent ions and examining the effect on the product ion. Ions can also be selectively ejected from the cell. These techniques, which were described in this thesis after an outline of the basic principles of ion cyclotron resonance spectroscopy, allow, one to unravel the gaseous ion chemistry in any chemical system. Rate constants of ion-molecule reactions can be determined by ion cyclotron resonance spectroscopy. The necessary equations, based on the equations relating measured peak intensities to ion currents, were derived and their limitations, as well as those of the experimental procedures for obtaining the input parameters for the expressions, were discussed. Rate constants can also be calculated theoretically and there are a few microscopic models which treat the collision of an ion with a polarizable neutral molecule (polarization model) or the unimolecular fragmentation of an intermediate complex (statistical models). Direct models, although more suitable for comparison with results from beam experiments, were presented together with the above mentioned models, and their importance for the interpretation of the basic aspects of ion-molecule chemistry was discussed. The ion cyclotron resonance spectrometer was used to study an acylation reaction in ketones, which seems to be general for carbonyl compounds. RCOR\'+ + RCOR\' &#8594; RCO+ (RCOR\') + R\'. Pressure plots of the ion currents in ketones allowed us to propose a mechanism according to which the acylated ketones are formed by the fragmentation of an excited dimer ion, in a fashion analogous to the fragmentation of ketone parent ions in ordinary mass spectroscopy. Steady state conditions prevail for the excited dimer, which can be stabilized at pressures high enough for the ion to collide with a neutral in a time short compared to his life time, thus relaxing excess energy. The acyl group can be transferred from a ketone of lower polarizability to one of higher polarizability; thus CH3CO+ is for instance transferred from acetone to butanone in a mixture of these two compounds, as detected by double resonance. Relative proton affinities of alcohols, acids, esters, and ketones were determined and the results are in agreement with the assumption of constant hydrogen affinity within a homologous series, as has been shown previously for the case of amines by others. Of particular interest is the following order of proton affinities: HCOOH < ( CH30H < C2H5OH < CH3COOH. The positive ion spectra of mixtures of acetic acid with methanol or ethanol revealed that this acid reacts with the alcohols yielding a protonated ester, in a process apparently analogous to the acid catalized esterification in solution. On the other hand,formic acid was found not to behave in this way, although the reactions are all exothermic. These results could be rationalized assuming that a nucleophilic attack takes place on the protonated acid by the alcohol. If the alcohol is more basic, only proton transfer is observed. Transesterification reactions were not detected, but this failure was compensated by a reaction which all higher alcohols, namely those capable of producing a secondary or tertiary carbonium ion, undergo with the esters. This reaction can be exemplified by (CH3)2CHOH2+ + HCOOC3H7 &#8594; HCO2(C3H7) (C3H7)+ + H2O. Although in this particular reaction both alkyl groups seem equivalent, they are not so with respect to internal vibrational energy; this was demonstrated by the decomposition reactions which the ionic products like the one in the reaction above undergo: the alkyl group originally in the alcohol is always eliminated. All the reactions mentioned above, namely, acylation of ketones, proton transfer, and esterification, show the importance of ion-molecule reaction studies in the gas phase, where the intrinsic properties of the reacting species can be examined, free from solvation effects. This point has been repeatedly stressed. In a last chapter in this thesis the necessary modifications of the ion cyclotron resonance spectrometer, in order to operate it in a pulsed mode, were described. With this kind of operation a bunch of ions is formed by a pulse of the electron beam and the ions react for a known period of time, after which they are removed from the cell. Kinetic studies can be more easily carried out in this way than in the conventional one. Some preliminary results were shown.

Silylamide ligands have been used throughout the Periodic Table since the 1960s. They have delivered landmark complexes by providing the first three co-ordinate f-element complexes, the first trigonal planar f-element complexes and the first near-linear f-element complexes. This area is reviewed in Chapter 2.Herein, this work presents the first uses of several novel bis-silylamide ligands developed at Manchester which take the form {N(SiR3)2} where R = Me, iPr or tBu to afford four novel ligands: N ʹ, {N(SiMe3)(SiiPr3)}; N**, {N(SitBuMe2)2}; N* {N(SitBuMe2)(SiiPr3)}; and N , {N(SiiPr3)2}. Group 1 and 2 complexes of all of these ligands are presented along with the previously reported N*ʹ [N*ʹ = {N(SitBuMe2)(SiMe3)}]; which show variable bonding motifs based on the steric bulk. The N** and N ligands have formed the bulk of the work presented and were used to stabilise the first trigonal planar actinide complex [U(N**)3], as well as the first near-linear Ln(II) (Ln = lanthanide) complexes [Ln(N )2] (Ln = Sm, Eu, Yb, Tm). Additionally the trigonal planar Ln(II) complexes [K(2.2.2-cryptand)][Ln(N**)3] (Ln = Sm, Eu, Yb, Tm) have also been synthesised to compare the physicochemical properties of trigonal planar and near-linear geometries on the same elements with similar ligands.

Polysialylated NCAM (polySia-NCAM) is re-expressed in a number of tumours, including small cell lung carcinoma and neuroblastoma and is strongly associated with aggressive, invasive and metastatic tumours in the clinic. SiRNA knockdown of the polysialyltransferases (polySTs), the enzymes responsible for polysialylation of neural cell adhesion molecule (NCAM), has been shown to abolish cell migration. PolySia-NCAM is thus a highly attractive novel therapeutic target. A library of potential polyST inhibitors has been synthesised, using substrate-based design and computational chemistry. Compounds synthesised include N-acylmannosamine analogues, thio-linked CMP-sialic acid analogues, N-acyl modified sialic acids and compounds incorporating elements of both approaches. Novel methodology development in the synthesis of many of the compounds is described, notably a novel route to N-acyl sialosides. In addition, compounds identified from in silico screening were considered. Routes to synthesis and isolation of analogues of biologically active compounds are described. Using an enzyme assay, compounds were evaluated for their ability to reduce polySia synthesis through polyST inhibition. Effects of agents on polySia expression in cells, and the ability of compounds to reduce cell migration in vitro was studied using a wound healing ‘scratch assay’. The data from these experiments revealed a number of potent modulators of polySia assembly and their efficacy in reducing cell migration, as well as the limits of the biosynthetic pathway to accept unnatural sialic acid precursors. This is the first example of polyST inhibition modulating tumour cell migration, and points to the potential of the polysialyltransferases as a therapeutic target in metastatic tumours.

Small molecule walkers developed to date take advantage of the reversibility of dynamic covalent bond formation to transport molecular fragments along molecular tracks using both diffusion processes and ratchet mechanisms. However, external intervention (the addition of chemical reagents and/or irradiation with light) is required to mediate each step taken by the walker unit in systems reported so far. In this Thesis, the first synthetic small molecule able to walk back-and-forth upon an oligoethylenimine track without external intervention via intramolecular Michael and retro- Michael reactions is described. The 1D random walk is highly processive and exchange takes place between adjacent amine groups in a stepwise fashion. The walker is used to perform a simple task: quenching of the fluorescence of an anthracene group situated at one end of the track as a result of the walking progress. In the presence of excess of base, the molecule preferentially ‘walks’ towards the favoured final foothold of tracks of increasing length and it is possible to monitor the population of all or a few positional isomers over time. In each case the molar fraction of walkers reaching the final foothold is determined quantitatively by 1H NMR. Control over the rate of exchange is achieved by varying the amount of base added. The dynamic migration of a small molecule upon the track is a diffusion process limited to one dimension and as such can in principle be described using the one dimensional random walk. Chapter I identifies a set of fundamental walker characteristics and includes an overview of the DNA-based and small molecule transporting systems published to date. Chapter II describes the inspiration for this work and model studies which lay the groundwork for the research presented in this thesis. The initial track architecture and optimisation of reaction conditions are demonstrated using a simple model compound which then led to the development and a detailed investigation of a first synthetic small molecule able to walk upon an oligoethylenimine track without external intervention. Chapter III presents a modified synthetic route towards the desired walker-track architectures and a comprehensive investigation of the dynamic properties of a series of tracks of increasing length upon which the walker migrates in a unidirectional fashion. The Outlook contains closing remarks about the scope and significance of the presented work as well as ideas for the design of novel small-molecule walkers, some of which are well under way in the laboratory. Chapter II (with the exception of model studies included at the beginning of the chapter) is presented in the form of article that has recently been published. No attempt has been made to re-write this work out of context other than merging content of the article with the supplementary information published together with the article. Chapter II is reproduced in the Appendix in its published format.

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / This dissertation describes single-molecule tracking (SMT) studies for the quantitative characterization of one-dimensional (1D) solvent-filled surfactant-templated mesoporous silica (STMS) materials and other nanostructured materials, such as double-stranded DNA. SMT permits the simultaneous and quantitative assessment of the nanoscale and microscale morphologies and mass-transport properties of the materials with nanometer-scale spatial resolution. The efficiency and selectivity of catalytic reactions and chemical separations occurring in liquid-filled mesoporous materials are governed by the translational and orientational mobilities and surface interactions of the incorporated reagents and analytes. Polarization dependent SMT results demonstrate that the dye molecules used as probes of materials nanostructure are tightly confined within the one-dimensional (1D) pores of surfactant-templated mesoporous silica films. Spectroscopic single molecule tracking (sSMT) data reveal that the hydrophobic probe dyes are confined within nonpolar regions of the nanomaterials For this dissertation, surfactant templated mesoporous silica films were prepared by the spin coating of acid catalyzed tetramethoxysilane (TMOS)-based silica sols on glass substrates in the presence of Cetyltrimethylammonium bromide (CTAB). Cylindrical CTAB micelles formed during evaporation of the solvent acted as a structure directing template, forming nanometer-sized one-dimensional pores within the silica films. SMT experiments were performed using a wide-field fluorescence microscope that was sufficiently sensitive to allow detection of the fluorescence from individual dye molecules. A series of perylene diimide (PDI) dyes was employed for basic structural characterization of the silica materials. Single molecule fluorescence was recorded in the form of fluorescence videos. These videos revealed the presence of immobile dye molecules, along with those diffusing in one and two dimensions (1D and 2D). The 1D diffusing molecules provided basic evidence for the confinement mass transport of the dye molecules within the silica mesopores. Spectroscopic single molecule tracking (sSMT) studies served as an extension of basic SMT experiments and were employed to determine the location of the molecules. The polarity sensitive dye Nile Red (NR) was employed in these studies. It exhibits 1D diffusion, consistent with its confinement to the cylindrical pores, as was also the case for the PDI dyes. The sSMT data revealed that the majority of NR molecules were found in nonpolar environments having polarities similar to that of n-hexane. Single molecule emission polarization (SMEP) measurements were employed to explore the orientational confinement of the dyes. The results of these experiments demonstrated that the PDI and NR molecules diffuse with their long axes aligned parallel to the long axis of the pores. All of the dyes employed were found to be orientationally confined to ∼1 nm diameter pathways within the pores. The diffusion coefficient for the dyes was also shown to be ∼10^3 -fold smaller than in bulk solution. The results of the NR studies demonstrate that the dye molecules were confined to the hydrophobic cores of the micelles, and provide support for the conclusion that the PDI dyes are similarly confined. These studies afford an enhanced understanding of how nanostructuring of the pore-filling medium in solvent- and surfactant-filled mesoporous materials governs the mass transport and surface interactions of incorporated reagents and analytes. The dependence of molecular confinement on dye charge and structure was also explored in this dissertation. The confined translational and orientational motions of a series of four different PDI dyes diffusing along one dimension (1D) within individual cylindrical silica mesopores were investigated in these studies. Specifically, the motions of cationic and anionic PDI dyes were compared to those of two uncharged PDIs having different alkane tail lengths. All four dyes exhibited populations that were immobile, along with separate populations that diffused in either 1D or 2D. The anionic and cationic PDI dyes exhibited the largest and smallest populations, respectively, of immobile molecules, suggesting that electrostatic interactions between the charged dyes and the cationic surfactant head groups play a significant role in limiting molecular motion. The cationic and anionic PDI dyes also exhibit the largest populations of 2D diffusing molecules, suggesting they may more readily pass between the cylindrical micelles and through the silica pore walls. All four dyes also emit strongly polarized fluorescence as they move in 1D, indicating they are orientationally confined within the nanochannels. Nile Red dye was used to determine the dielectric constant, ε, of nonpolar microenvironments in double-stranded DNA (ds-DNA) single molecules both in aqueous buffer solution and when adsorbed on amine-modified chemical gradient surfaces. The value of ε within the DNA decreased with increasing buffer concentration. Values of ε ∼ 6.75 and ∼3.00 were obtained in 0.1 mM phosphate buffered saline (PBS) and in 10 mM PBS, respectively. Similar effects were observed upon adsorption to chemically graded amine-modified silica surfaces. Under 1 mM buffer, ε was measured to be ∼2.84 and ∼1.90 at the low amine (high silica), and high amine (low silica) ends of the gradient, respectively. An increase in the buffer concentration again led to a decrease in ε, but only at the low amine end. It is concluded that high buffer concentrations and binding to an amine surface cause condensation of the ds-DNA, forming less polar microenvironments within its structure. These results provide important knowledge of the factors governing the polarity of DNA microenvironments to which intercalators bind.

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.

G-quadruplexes are non-canonical nucleic acid secondary structures of increasing biological and medicinal interest due to their proposed physiological functions in transcription, replication, translation and telomere biology. Aberrant G4 formation and stabilisation have been linked to genome instability, cancer and other diseases. However, the specific genes and pathways involved are largely unknown, and the work within this thesis aims to investigate this. Stabilisation of G4s by small molecules can perturb G4-mediated processes and initial studies suggest that this approach has chemotherapeutic potential. I therefore also aimed to identify cell genotypes sensitive to G4-ligand treatment that may offer further therapeutic opportunities. To address these aims, I present the first unbiased genome-wide genetic screen in cells where genes were silenced via short-hairpin RNAs (shRNAs) whilst being treated with either PDS or PhenDC3, two independent G4-stabilising small molecules. I explored gene deficiencies that enhance cell death (sensitisation) or provide a growth advantage (resistance) in the presence of these G4-ligands. Additionally, I present a validation screen, comprising hits uncovered via genome-wide screening, and also the use of this in another cell line of different origin. Sensitivities were enriched in DNA replication, cell cycle, DNA damage repair, splicing and ubiquitin-mediated proteolysis proteins and pathways. Ultimately, I uncovered four synthetic lethalities BRCA1, TOP1, DDX42, GAR1, independent of cell line and ligand. These were validated with three G4-stabilising ligands (PDS, PhenDC3 and CX-5461) using an independent siRNA approach. The latter siRNA methodology was used to screen 12 PDS derivatives with improved medicinal chemistry properties and ultimately identified SA-100-128, as a lead compound. The mechanism behind synthetic lethality with G4-stabilising ligands was explored further for DDX42, which I show has in vitro affinity for both RNA- and DNA-G4s and may represent a previously unknown G4-helicase. Also within this thesis, gene deficiencies that provided a growth advantage to PDS and/or PhenDC3 as uncovered by genome-wide and focused screening were explored. These showed enrichment in transcription, chromatin and lysosome-associated genes. The resistance phenotype of three gene deficiencies, TAF1, DDX39A and ZNF217 was further supported by additional siRNA experiments. Overall, I satisfied the primary aims and established many novel synthetic lethal and resistance interactions that may represent new therapeutic possibilities. Additionally, the results expand our knowledge of G4-biology by identifying genes, functions and subcellular locations previously not known to involve or regulate G4s.

No description available.