In the development of noninvasive optical biopsy, normal tissues can be statistically differentiated from precancerous and cancerous tissues by analyzing their autofluorescence spectra. The observed cancer hallmarks in the spectra are manifestations of biochemical and morphological changes in tissue during cancerous transformation. For detection of colorectal cancers, it has been hypothesized that the major contributors to tissue fluorescence are three endogenous fluorophores – reduced nicotinamide adenine dinucleotide (NADH), flavin adenine dinucleotide (FAD) and collagen. Separating and identifying endogenous fluorophores in cells/tissues using capillary electrophoresis (CE) with laser–induced fluorescence (LIF) detection holds promise as a simple and fast method to analyze fluorophore compositions in tissues during the cancerous transformation. To this end, we have established the extraction and separation protocols for quantifying endogenous fluorophores in Chinese Hamster Ovary (CHO) cells, human colorectal adenocarcinoma cells (HT–29) and human normal colon cells (FHC). Flavin mononucleotide (FMN), FAD, NADH and nicotinamide adenine dinucleotide phosphate (NADPH) have been identified in the cell extracts by spiking them with standards and quantified by standard addition methods. The influence of cell densities and cell growth stages on fluorophore composition has been closely examined. Two–dimensional (2D) correlation coefficient mapping of electropherograms of HT–29 and FHC cell extracts reveals that the HT–29 cell extracts with higher cell density can be differentiated from FHC and HT–29 cell extracts with lower cell density, which is also demonstrated by the comparison of peak area ratios of NADH and NADPH. The electropherograms for 2D correlation analysis are pretreated by aligning their prominent peaks to account for peak shifting. A challenge in biological spectroscopy of cells and tissue is the identification of endogenous components that contribute to the overall complex spectra and the diagnostic signature. We propose 2D generalized correlation of CE–LIF electropherograms and fluorescence spectra in order to resolve the overlapped fluorescence spectra into their individual components. Separation of the endogenous fluorophores in normal and cancer cells by CE–LIF has provided us insight into fluorophore compositions and tools for classifications of cells. It has also prepared us for extraction and separation of tissues under different physiological conditions to assist cancer diagnosis.

Methylation of CpG islands located at the promoter regions is a mechanism which controls gene silencing and expression. Hyper or hypo methylation of these sites on promoter sequences have been associated with many diseases, like cancer. Even though promoter CpG islands and their methylation profiles are important regulators of gene expression, the exact mechanism of gene silencing through methylation is not known. Here, we have investigated the status of promoter CpG methylation under various evolutionary pressures by calculating the differences in promoter CpG content and methylation profiles at different pass points. In order to determine the list of genes under each category we have analyzed and compared the orthologs among 58 genomes available through ENSEMBL. The total number of CpG dinucleotides at the promoter regions of all groups of genes have been calculated and compared. Additionally, we have compared the experimentally determined methylation profiles of these CpG&#039 / s between human blood cells and fibroblast cells. While the promoter CpG content changed through common to newer genes, the number of the CpG units methylated found to be consistent. Here, we present the functional level analysis of common gene lists at different pass points and report the differences of the promoter CpG content and the methylation profiles among these groups with distinct evolutionary conservation status. We have also observed the conservation status of individual methylated CpG units on the low and high methylated genes. Our analysis revealed that the surrounding methylation content had a positive effect on the conservation of individual CpG&rsquo / s.

Dissociation constants for alternate dirmcleotide substrates and competitive inhibitors suggest that the dinucleotide binding site of the Ascaris suum NAD-malic enzyme is hydrophobic in the vicinity of the nicotinamide ring. Changes in the divalent metal ion activator from Mg^2+ to Mn^2+ or Cd^2+ results in a decrease in the dinucleotide affinity and an increase in the affinity for malate. Primary deuterium and 13-C isotope effects obtained with the different metal ions suggest either a change in the transition state structure for the hydride transfer or decarboxylation steps or both. Deuterium isotope effects are finite whether reactants are maintained at saturating or limiting concentrations with all the metal ions and dinucleotide substrates used. With Cd^2+ as the divalent metal ion, inactivation of the enzyme occurs whether enzyme alone is present or is turning over. Upon inactivation only Cd^2+ ions are bound to the enzyme which becomes denatured. Modification of the enzyme to give an SCN-enzyme decreases the ability of Cd^2+ to cause inactivation. The modified enzyme generally exhibits increases in K_NAD and K_i_metai and decreases in V_max as the metal size increases from Mg^2+ to Mn^2+ or Cd^2+, indicative of crowding in the site. In all cases, affinity for malate greatly decreases, suggesting that malate does not bind optimally to the modified enzyme. For the native enzyme, primary deuterium isotope effects increase with a concomitant decrease in the 13-C effects when NAD is replaced by an alternate dinucleotide substrate different in redox potential. This suggests that when the alternate dinucleotides are used, a switch in the rate limitation of the chemical steps occurs with hydride transfer more rate limiting than decarboxylation. Deuteration of malate decreases the 13-C effect with NAD for the native enzyme, but an increase in 13-C effect is obtained with alternate dinucleotides. These suggest the presence of a secondary 13-C effect in the hydride transfer step. This phenomenon is also applicable to the modified enzyme with NAD as the substrate.

Nucleic acids, such as DNA, play an essential role in all known forms of life; however, despite their fundamental importance, there is still a significant lack of understanding surrounding their functional behaviour. This thesis explores the structure and dynamics of DNA by employing methods based on fluorescence and through the use of computational calculations. Time-resolved fluorescence experiments have been performed on dinucleotides containing 2-aminopurine (2AP) in various alcohol-water mixtures. 2AP, a fluorescent analogue of the nucleobase adenine, has been used extensively to investigate nucleic acids because of its ability to be incorporated into their structures with minimal perturbation and its high sensitivity to its local environment. Direct solvent effects on 2AP were established through measurements on the free fluorophore. Analysis of the complex fluorescence decays associated with the dinucleotides was challenging but has provided insight into their conformational dynamics. Solvent polarity was found to play a significant role in determining both photophysical and conformational properties in these systems. The complicated fluorescence decay of 2AP in nucleic acids highlights the need for accurate and unbiased analysis methods. Various time-resolved fluorescence analysis methods, including iterative reconvolution and the exponential series method, have been investigated with real and simulated data to obtain an overview of their benefits and limitations. The main outcome of the evaluation is that no single method is preferred in all situations and there is likely to be value in using a combination when there is ambiguity in the interpretation of the results. Regardless of the analysis technique used, the parameterised description of the observed fluorescence decay is meaningless if the underlying physical model is unrealistic. The advance of computational methods has provided a new means to rigorously test the viability of proposed models. Calculations have been performed at the M06-2X/6-31+G(d) level of theory to investigate the stability of 2AP-containing dinucleotides in conformations similar to those observed in the double-helical structure of DNA. The results help to explain the similarity of the time-resolved fluorescence behaviour of 2AP in dinucleotide and DNA systems but also bring to light subtle differences that could perhaps account for experimental discrepancies. The recent emergence of advanced optical microscopy techniques has offered the prospect of being able to directly visualise nucleic acid structure at the nanoscale but, unfortunately, limitations of existing labelling methods have hindered delivery of this potential. To address this issue, a novel strategy has been used to introduce reversible fluorescence photoswitching into DNA at high label density. Photophysical studies have implicated aggregation and energy-transfer as possible quenching mechanisms in this system, which could be detrimental to its future application. The reliability of fluorescence photoswitching was investigated at ensemble and single-molecule level and by performing optical lock-in detection imaging. These developments lay the foundations for improved and sequence-specific super-resolution microscopy of DNA, which could offer new insights into the 3D nanoscale structure of this remarkable biopolymer. In summary, the work presented in this thesis outlines important observations and developments that have been made in the study of the structure and dynamics of nucleic acids.

<p>  </p> <p>Cyclic dinucleotides (CDNs) such as the bacterial CDNs (cyclic-di-AMP, cyclic-di-GMP and 3’3’cyclic GMP-AMP) and mammalian CDN, 2’3’-cGAMP, are essential immune response second messenger signaling molecules. These CDNs act via Stimulator of interferon genes (STING)-TANK Binding Kinase 1 (TBK1)-Interferon Regulatory Factor 3 (IRF3) pathway. However, data from our lab and others indicate that beyond the classical STING-TBK1-IRF3 pathway, CDNs also regulate other signaling axes related to both inflammatory and non-inflammatory pathways. But, a global view of how these CDNs affect signaling in diverse cells or through non-STING pathways is lacking. There is also paucity of data on CDN modulated kinases and no global assessment of phosphorylation events that follow cyclic GMP AMP synthase (cGAS)-STING axis stimulation in immune cells. Herein, I have used a proteomics approach to determine signaling pathways regulated by bacterial CDNs, c-di-GMP and c-di-AMP in human gingival fibroblasts such as pathways related to nucleotide excision repair (NER) which ordinarily do not channel through STING (Chapter 3). Additionally, with the use of phosphoproteomics and bioinformatics, this project accomplished a system-wide phosphorylation analyses of T cells treated with 2’3’cGAMP and showed that 2’3’cGAMP impact various, yet unreported critical kinases (E.g. LCK, ZAP70, ARG2) and signaling pathways important for T cell function (Chapter 4). Asides known interferon signaling, these differentially phosphorylated kinases were involved in T cell receptor (TCR) signaling, myeloid cell differentiation, cell cycle regulation, and regulation of double strand break repair. </p> <p>Another area of interest addressed by this project is the discovery of novel antibacterial agents against multi-drug resistant (MDR) bacteria. Thus, in Chapters 5 and 6, I show the identification, antibacterial activity and characterization of <strong>HSD1835</strong> and <strong>HSD1919 </strong>as novel SF5 and SCF-containing membrane active compounds, highly potent against preformed MDR biofilms with fast bactericidal activity against persister bacteria. Plus, an exciting addition to the fight against MDR bacteria in Chapter 7, the discovery of <strong>HSD1624</strong> and analogs, which are able to re-sensitize MDR and colistin resistant bacteria such as <em>Pseudomonas aeruginosa</em> from a colistin MIC of 1024 μg/mL to 0.03 μg/mL (64000-fold reduction). Ultimately, these compounds could be translated into anti-biofilm and, anti-MDR bacteria therapeutics, preventing repeated surgeries due to infections, and saving lives. </p>

La Tomographie par émission de positons (TEP) constitue l’une des techniques d’imagerie médicale les plus novatrices pour la visualisation in vivo des processus biologiques. Elle intervient comme technique de choix pour le diagnostic dans de nombreux domaines notamment, en oncologie, cardiologie ou encore en neurologie. La conception et l’élaboration de nouveaux radiotraceurs sont en perpétuel développement. L’utilisationd’oligonucléotides (ODN) modifiés (aptamères) possédant une grande affinité et spécificité pour une cible (gène,protéine, principe actif), comme radiotraceur pour l’imagerie in vivo apparait comme une alternative intéressante. A ce jour, quelques rares exemples d’oligonucléotides marqués, par un radioisotope, ont été décrits dans la littérature.Dans ce contexte, il a été développé deux méthodologies d’introduction du radioisotope (11C ou 18F) en dernièreétape de synthèse par chimie ‘‘click’’ pour le marquage de nucléosides et d’oligonucléotides envisagés commeradiotraceurs pour la TEP. / Positron Emission Tomography (PET) is a powerful molecular-imaging technique for physiological and biologicalinvestigations in various areas, such as oncology, cardiology, and neurosciences, as well as for drug development.Due to the increasing need of this technique for in vivo applications, there is always a demand for the developmentof new tracers and radiolabeling strategies. Furthermore, because of their excellent targeting capacities and easysynthesis along with a high level of diversity, oligonucleotides are already extensively used in vitro as ligands fornucleic acids (antisense oligonucleotides), proteins, and small related molecules (aptamer oligonucleotides). Theuse of aptamers for in vivo imaging appears especially promising, because of the wide range of possibilitiesavailable to introduce variations in their structure through defined chemical modifications. However, only fewexamples of oligonucleotide labeling for PET have been reported. In this context, we have developed twomethodological ways to introduce the radioisotope (11C, 18F), by ‘‘click’’ chemistry, at the last radiosynthesis stepin order to label nucleoside and oligonucleotide as potential radiotracers for PET.

Le couplage de Stille modifié développé par l’équipe du Pr Fouquet a été appliqué à la méthylation de nucléosides, dinucléotides et oligonucléotides dans le but de mettre au point une méthodologie de marquage d’aptamères au carbone 11 pour le diagnostic précoce de cancer par TEP. Ce couplage pallado-catalysé est basé sur l’utilisation de monoorganoétain activé par une source de fluorure permettant d’accélérer la réaction. Dans un premier temps, les essais méthodologiques ont permis de mettre au point le transfert de groupement méthyle sur différents nucléosides et un dinucléotide modifiés dans des conditions compatibles avec la durée de demi-vie du carbone 11 (20,4 min) et la nature particulière des oligonucléotides. Puis, cette méthodologie a été appliquée à des oligonucléotides modèles obtenus après incorporation des nucléosides les plus prometteurs. / The modified Stille cross-coupling developed by Pr. Fouquet’s group was applied to the methylation of nucleosides, dinucleotides and oligonucleotides in order to develop a methodology for labelling aptamers with carbon 11 for the early diagnosis of cancer by PET. This pallado-catalyzed cross-coupling is based on the use of monoorganotin activated by a source of fluoride accelerating the reaction. Initial methodology tests helped to finalize the transfer of methyl group on various nucleosides and a dinucleotide, with reaction conditions compatible with the short half-life of carbon 11 (20.4 min) and the special nature of oligonucleotides. Then, this methodology was applied to oligonucleotide models obtained after incorporation of the most promising nucleosides.

Genome composition and architecture is shaped by two types of processes: those that introduce heritable changes (mutagenesis) and those that determine the fate of such changes in the populations (genetic drift and selection). Chemical and biological properties of mutagenesis determines the frequencies at which different type of mutations occur, which, in turn, determines their rates of fixation by drift and affects the spectrum of mutations available for selection to operate on. As the result, genomes of living organisms carry many signatures mutagenesis.