Estudos envolvendo o oxigênio molecular singlete (1O2) tem uma relevância biológica, uma vez que esta espécie, devido ao caráter eletrofílico, reage com moléculas ricas em elétrons como proteínas, lipídeos e DNA provocando danos que resultam em perdas de função e integridade celular. Em sistemas biológicos, a presença de outras espécies reativas de oxigênio e nitrogênio, dificultam a identificação de lesões específicas causadas por 1O2 .Neste contexto, este trabalho foi desenvolvido objetivando a síntese de endoperóxidos isotopicamente marcados com 17O para serem utilizados como fonte geradora limpa de 17[1O2] em estudos mecanísticos. A capacidade de geração de 17[1O2] pelo endoperóxido N,N\'-di(2,3-dihidroxipropil)-3,3\'-(1,4 naftilideno) dipropanamida 17O (DHPN17O2) foi confirmada utilizando o captador químico sulfato mono-{2-[10-(2-sulfoxi-etil)-antracen-9-il]-etil}éster de sódio e o nucleosídeo 2\'- desoxiguanosina. Os produtos isotopicamente marcados com 17O formados foram analisados por espectrometria de ressonância magnética nuclear e cromatografia líquida de alta eficiência acoplado ao espectrômetro de massa. Os lipídeos, em especial o colesterol ao reagir com o 1O2 geram hidroperóxidos de colesterol como produtos de oxidação primária e na presença de metais resulta em compostos de maior reatividade e toxicidade, como os radicais peroxila, que contribuem para a propagação da peroxidação lipídica. Neste trabalho, demonstramos que os hidroperóxidos de colesterol são capazes de gerar 1O2 na presença de metal através de medidas de luminescência, utilização de supressores e captador químico de 1O2. Os mecanismos de reação envolvidos foram estudados e determinados por espectrometria de massa acoplada a cromatografia líquida de alta eficiência. Por fim, a caracterização detalhada dos produtos formados por espectrometria de ressonância magnética nuclear e massa na reação do colesterol com 1O2 mostrou que além dos hidroperóxidos a reação também produz um aldeído, o 3&#946; -hidroxi-5&#946;-hidroxi-B-norcolestano-6&#946;-carboxialdeído. Até o momento, este composto havia sido identificado como um produto específico da ozonização do colesterol. Neste estudo, baseado nos estudos por reações de quimiluminescência, é proposto o mecanismo de formação deste aldeído em reações de oxidação de colesterol por 1O2 envolvendo intermediário dioxetano. / Studies involving singlet molecular oxygen (1O2) has biological relevance, once this species, due to its eletrophylic character, reacts with rich electron molecules such as proteins, lipids and DNA causing damages that result in loss of function and cellular integrity. In biological system, the presence of other reactive species of oxygen and nitrogen impair the identification of lesions caused by 1O2. In this context, this work was developed with the aim of synthesizing <SUP17O-labeleded endoperoxides to be used as a clean source of (1O2) in mechanistic studies. The ability of 17[1O2]generation by N,N\'-di(2,4-dihydroxypropyl)-1,4-naphthalene-dipropanamide labeled with 17O(DHNP17O2) was observed using the disodium salt of anthracene-9,10-diyldiethyl disulfate as a chemical trap and the nucleoside 2\'-deoxyguanosine. The products isotopically labeled with 17O were analyzed by nuclear magnetic resonance spectroscopy and high performance liquid chromatography coupled to a mass spectrometer. Lipds, in special the cholesterol, when reacting with singlet molecular oxygen generate cholesterol hydroperoxides as primary products and in the presence of metals result in compounds of higher reactivity and toxicity, such as peroxyl radicals which contribute to the propagation of lipid peroxidation. In this work, we demonstrated that cholesterol hydroperoxides are able to generate singlet molecular oxygen in the presence of metal by chemiluminescence measurements by testing the effect of singlet molecular oxygen quencher and by chemical trap. The involved reaction mechanisms were studied and determined by mass spectrometry coupled to the high performance liquid chromatography. Finally, we detailed characterization of the products formed in the reaction of cholesterol with 1O2 by nuclear magnetic resonance and mass spectroscopy showed that besides cholesterol hydroperoxides, the reaction also produces an aldehyde, 3&#946;hydroxy-5&#946;-hydroxy-B-norcholestan-6&#946;-carboxyaldehyde which had been identified as a specific product of cholesterol ozonization. In this study, based on the studies of chemiluminescence reactions, the mechanism of formation of this aldehyde in reaction of oxidation of cholesterol by 1O2 involving a dioxetane intermediate has been proposed.

Submitted by Geandra Rodrigues (geandrar@gmail.com) on 2018-01-09T14:43:53Z No. of bitstreams: 1 rafaelmarques.pdf: 2550703 bytes, checksum: 4694887625f47f1d8d4f3dbed5d78f1d (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2018-01-23T11:20:19Z (GMT) No. of bitstreams: 1 rafaelmarques.pdf: 2550703 bytes, checksum: 4694887625f47f1d8d4f3dbed5d78f1d (MD5) / Made available in DSpace on 2018-01-23T11:20:19Z (GMT). No. of bitstreams: 1 rafaelmarques.pdf: 2550703 bytes, checksum: 4694887625f47f1d8d4f3dbed5d78f1d (MD5) Previous issue date: 2017-09-29 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Esta tese de doutorado aborda o preparo, a caracterização e a utilização de fases estacionárias monolíticas para uso em colunas de separação cromatográfica em escala capilar. As fases estacionárias foram preparadas pela polimerização do monômero 3-(metacriloxipropil)-trimetoxisilano em duas etapas envolvendo primeiramente um processo sol-gel e depois um processo de adição radicalar fotoiniciado. A fotopolimerização foi feita in situ em capilares de sílica fundida transparentes à radiação UV com 100 μm de diâmetro interno. As colunas produzidas foram aplicadas qualitativamente com sucesso na separação de cinco hidrocarbonetos policíclicos aromáticos e três hormônios esteroides, tanto por cromatografia a líquido capilar quanto por eletrocromatografia capilar em um equipamento de eletroforese capilar. A eletrocromatografia foi usada para analisar quantitativamente uma amostra de emulsão transdérmica contendo estriol e 17-β-estradiol. Como tentativa de melhorar a separação entre alguns analitos, foi feita a modificação do polímero adicionando o monômero benzil metacrilato, porém sem sucesso. As colunas foram caracterizadas com relação à sua homogeneidade física usando um microscópio óptico e um detector condutométrico sem contato capacitivamente acoplado. O detector foi usado como um scanner não invasivo deslocando-se longitudinalmente ao longo da coluna externamente ao capilar. A caracterização química do polímero foi feita através da espectroscopia de ressonância magnética nuclear no estado sólido dos núcleos de 13C e de 29Si. Foi possível propor uma estrutura para o arranjo da cadeia carbônica e o grau de substituição do grupo silil indicando a reticulação das cadeias poliméricas através da formação de dímeros e trímeros condensação de grupos alcoxisilanos. / This doctoral thesis adresses the preparation, characterization and use of monolithic stationary phases for chromatographic separation columns in capillary scale. The stationary phases were prepared by polymerizing the 3- (methacryloxypropyl) trimethoxysilane monomer in two steps involving a sol-gel process followed by a photoinitiated radical addition. The photopolymerization was carried out in UV transparent coating fused silica capillaries with 100 μm of internal diameter. The columns were applied in the qualitative separation of five polycyclic aromatic hydrocarbons and three steroid hormones, both by capillary liquid chromatography and capillary electrochromatography in a capillary electrophoresis equipment. Electrochromatography was used to quantitative analyzis of a transdermal emulsion sample containing estriol and 17-β-estradiol. In an attempt to improve the separation between some analytes, the polymer was modified by adding the benzyl methacrylate monomer, but without success. The columns were characterized with respect to their physical homogeneity using an optical microscope and a capacitively coupled contactless conductivity detector. The detector was used as a non-invasive scanner moving longitudinally along the column externally to the capillary. The chemical characterization of the polymer was done by the solid state 13C and 29Si nuclear magnetic resonance spectroscopy. It was possible to propose a carbon chain strucuture and the substitution degree of the silyl group indicating the cross-linking of the polymer chains through the formation of dimers and trimers by condensation of the alkoxysilane groups.

This thesis uses solid-state nuclear magnetic resonance (NMR) spectroscopy and density functional theory (DFT) calculations to study local structure and disorder in inorganic materials. Initial work concerns microporous aluminophosphate frameworks, where the importance of semi-empirical dispersion correction (SEDC) schemes in structural optimisation using DFT is evaluated. These schemes provide structures in better agreement with experimental diffraction measurements, but very similar NMR parameters are obtained for any structures where the atomic coordinates are optimised, owing to the similarity of the local geometry. The ³¹P anisotropic shielding parameters (Ω and κ) are then measured using amplified PASS experiments, but there appears to be no strong correlation of these with any single geometrical parameter. In subsequent work, a range of zeolitic imidazolate frameworks (ZIFs) are investigated. Assignment of ¹³C and ¹⁵N NMR spectra, and measurement of the anisotropic NMR parameters, enabled the number and type of linkers present to be determined. For ¹⁵N, differences in Ω may provide information on the framework topology. While ⁶⁷Zn measurements are experimentally challenging and periodic DFT calculations are currently unreliable, calculations on small model clusters provide good agreement with experiment and indicate that ⁶⁷Zn NMR spectra are sensitive to the local structure. Finally, a series of pyrochlore-based ceramics (Y₂Hf₂₋ₓSnₓO₇) is investigated. A phase transformation from pyrochlore to a disordered defect fluorite phase is predicted, but ⁸⁹Y and ¹¹⁹Sn NMR reveal that rather than a solid solution, a significant two-phase region is present, with a maximum of ~12% Hf incorporated into the pyrochlore phase. The use of ¹⁷O NMR to provide insight into the local structure and disorder in these materials is also investigated. Once the different T₁ relaxation and nutation behaviour is considered it is shown that quantitative ¹⁷O enrichment of Y₂Sn₂O₇ is possible, and that ¹⁷O does offer a promising future tool for study.

The development of synthetic molecular receptors that can selectively bind anions, translocate them through a lipidic bilayer membrane and release them on the other side is a very topical and emerging field of supramolecular chemistry, warranted by the biological importance of transmembrane anion transport.The first part of this thesis is devoted to the study of the transmembrane transport of chloride and of the organic ion pair propylammonium chloride with calix[6]arene receptors functionalized with three (thio)urea arms on their small rim. The transport of chloride across the lipid bilayer of liposomes was monitored by fluorescence spectroscopy using the lucigenin assay. We report the first example of calix[6]arenes able to act as mobile carrier for the transport of chloride via a Cl-/NO3- antiport. We furthermore show that our calixarene systems are able to perform the cotransport of propylammonium chloride, with the chloride bound at the level of the (thio)urea groups and the ammonium included in the calixarene cavity. To provide direct proof of cotransport, we developed a 1H NMR methodology involving a thulium- complex shift reagent with which we were able to distinguish the signals of the ammonium transported inside the liposomes from those of the external ammonium. We also highlight the role of the complexing calixarene cavity for the cotransport by comparing the calixarenes to known transporters deprived of a cavity. The transmembrane transport organic ion pairs could find applications in the transport of biologically relevant ammonium compounds such as catecholamines and amino acids. Our results are reported in the publication “Repositioning Chloride Transmembrane Transporters: Transport of Organic Ion Pairs” Grauwels, G. Valkenier, H. Davis, A. P. Jabin, I. Bartik, K. Angew. Chemie - Int. Ed. 2019, 58, 6921–6925.The second part of this thesis is devoted to the study of binding of chloride to receptors embedded in a lipid membrane, the first step of the transmembrane transport process. Both 1H and 31P NMR spectroscopy proved to be inadequate to study the binding using liposomes or micelles as model membranes. With liposomes, the NMR signals are too broad to be exploited and in the case of micelles, the competition between the lipid headgroups and chloride made it impossible to obtain a NMR signature which unambiguously characterizes chloride binding. The 35Cl NMR signal is on the other hand strongly affected by the presence of anion receptors, both in organic solvents and when incorporated lipid bilayers. We developed a methodology to evaluate the binding of chloride, based on the monitoring of the chloride linewidth during titration experiments. A linear relationship between the linewidth and the concentration of receptors is observed and the slopes can be exploited to compare the binding strengths of different structurally related receptors. We show that 35/37Cl NMR is a versatile tool which can help in the understanding and development of new transporters by providing new insights of the physicochemical understanding of the transport process. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

La gélification est un phénomène courant dans lequel une grande quantité de solvant est immobilisée dans un réseau constitué de relativement petites quantités de substrat. Avec des propriétés à la fois solides et liquides, un gel est un état unique. L'étude des propriétés et du mécanisme de la gélification attire l'attention des chercheurs du monde entier. Cependant, de nombreuses questions restent en suspens, telles que le processus d'auto-assemblage et les interactions moléculaires dans le système de gel, la relation entre les solutions, les gels et les cristaux et l'organisation moléculaire dans le réseau de gel. L'exploration de ces questions fournira des connaissances sur le mécanisme de gélification et contribuera à la conception et à la fabrication de nouveaux gels aux applications diverses. Cette thèse décrit notre étude des gels et de leur relation avec les solutions et les cristaux à l'aide de sels biliaires, qui sont des molécules amphiphiles naturelles abondantes. La rigidité de la partie stéroïde et l'hydrophobie variable des sels biliaires facilitent l'étude du processus d'autoassemblage. La recherche est présentée à travers trois articles publiés ou soumis au cours de mon programme de doctorat. Le premier article explore les interactions moléculaires qui se produisent dans la formation d'hydrogels moléculaires fabriqués à partir de mélanges de désoxycholate de sodium et d'acide formique. La spectroscopie de résonance magnétique nucléaire fournit de nouvelles informations sur la transition gel-sol au niveau moléculaire, l'interaction entre les espèces libres/gélifiées et l'interaction des régions hydrophobes des sels biliaires avec le réseau de gel. Le deuxième article résume notre exploration de la relation entre les gels et les cristaux, en particulier la façon dont les composants moléculaires sont organisés. Les sels d'ammonium d'acide lithocholique produisent différents modèles d'auto-assemblage, tels que des gels, des fibres et des cristaux, avec divers anions d'ammonium. L'organisation moléculaire de l’acide lithocholique dans différentes conditions est remarquablement cohérente, indiquant qu'il existe une relation intime entre la gélification et la cristallisation dans ce système. Les résultats ont également mis en lumière la question de longue date de l'agencement des molécules dans les fibres de gel. Le troisième article décrit notre étude systématique de la gélification et de la cristallisation en utilisant une gamme plus large de sels biliaires. Généralement, avec l'augmentation de iii l'hydrophobie des sels biliaires, la préférence pour la formation de solutions est progressivement remplacée par une tendance à produire des gels et finalement des cristaux. Une association bord à bord d'anions biliaires est également observée dans différents types de sels biliaires. Les résultats renforcent notre conclusion selon laquelle les structures moléculaires internes des fibres dans les gels et dans les cristaux sont étroitement liées. / Gelation is a common phenomenon in which a large amount of solvent is immobilized in a network made up of relatively small amounts of substrate. With properties of both solid and liquid, a gel is a unique state. Gelation draws attention from researchers worldwide to study its properties and mechanism. However, many questions are still unraveled, such as the self-assembly process and molecular interactions in the gel system, the relationship between solutions, gels, and crystals, and the molecular organization in the gel network. Exploring these questions will provide knowledge about the mechanism of gelation and contribute to the design and fabrication of new gels for different applications. This thesis describes our study of gels and their relationship with solutions and crystals using bile salts, which are abundant natural amphiphiles. The rigid steroid moiety and the variable hydrophobicity of the bile salts facilitate the study of the self-assembly process. The research is presented through three articles published or submitted during my Ph.D. program. The first paper probes the molecular interactions that occur in the formation of molecular hydrogels made from mixtures of sodium deoxycholate and formic acid. Nuclear magnetic resonance spectroscopy provides new information about the gel-sol transition on the molecular level, the interaction between free/gelated species, and the interaction of hydrophobic regions of bile salts with the gel network. The second paper summarizes our exploration of the relationship between gels and crystals, especially how the molecular components are organized. Ammonium salts of lithocholic acid produce different patterns of self-assembly, such as gels, fibers, and crystals, with various ammonium anions. The molecular organization of lithocholates under different conditions is remarkably consistent, indicating that there is an intimate relationship between gelation and crystallization in this system. The results also shed light on the long-existing question of how molecules are arranged in gel fibers. The third paper describes our systematic study of gelation and crystallization using a broader range of bile salts. Generally, with increasing hydrophobicity of the bile salts, the preference to form solutions is gradually superseded by a trend to produce gels and finally crystals. An edge-to-edge association of bile anions is also observed in different kinds of bile salts. The results strengthen our conclusion that the internal molecular structures of fibers in gels and in crystals are closely related.

Les interactions ARN/ARN de type kissing-loop sont des éléments de structure tertiaire qui jouent souvent des rôles clés chez les ARN, tant au niveau fonctionnel que structural. En effet, ce type d’interaction est crucial pour plusieurs processus dépendant des ARN, notamment pour l’initiation de la traduction, la reconnaissance des ARN antisens et la dimérisation de génome rétroviral. Les interactions kissing-loop sont également importantes pour le repliement des ARN, puisqu’elles permettent d’établir des contacts à longue distance entre différents ARN ou encore entre les domaines éloignés d’un même ARN. Ce type d’interaction stabilise aussi les structures complexes des ARN fonctionnels tels que les ARNt, les riborégulateurs et les ribozymes. Comme d’autres ARN fonctionnels, le ribozyme VS de Neurospora contient une interaction kissing-loop importante. Celle-ci est impliquée dans la reconnaissance du substrat et se forme entre la tige-boucle I (stem-loop I, SLI) du substrat et la tige-boucle V (stem-loop V, SLV) du domaine catalytique. Des études biochimiques ont démontré que l’interaction kissing-loop I/V, dépendante du magnésium, implique trois paires de bases Watson-Crick (W-C). De plus, cette interaction est associée à un réarrangement de la structure du substrat, le faisant passer d’une conformation inactive dite unshifted à une conformation active dite shifted. Les travaux présentés dans cette thèse consistent en une caractérisation structurale et thermodynamique de l’interaction kissing-loop I/V du ribozyme VS, laquelle est formée de fragments d’ARN représentant les tige-boucles I et V dérivées du ribozyme VS (SLI et SLV). Cette caractérisation a été réalisée principalement par spectroscopie de résonance magnétique nucléaire (RMN) et par titrage calorimétrique isotherme (isothermal titration calorimetry, ITC) en utilisant différents complexes SLI/SLV dans lesquels l’ARN SLV est commun à tous les complexes, alors que différentes variations de l’ARN SLI ont été utilisées, soit en conformation shiftable ou preshifted. Les données d’ITC ont permis de démontrer qu’en présence d’une concentration saturante de magnésium, l’affinité d’un substrat SLI preshifted pour SLV est extrêmement élevée, rendant cette interaction plus stable que ce qui est prédit pour un duplexe d’ARN équivalent. De plus, l’étude effectuée par ITC montre que des ARN SLI preshifted présentent une meilleure affinité pour SLV que des ARN SLI shiftable, ce qui a permis de calculer le coût énergétique associé au réarrangement de structure du substrat. En plus de confirmer la formation des trois paires de bases W-C prédites à la jonction I/V, les études de RMN ont permis d’obtenir une preuve structurale directe du réarrangement structural des substrats SLI shiftable en présence de magnésium et de l’ARN SLV. La structure RMN d’un complexe SLI/SLV de grande affinité démontre que les boucles terminales de SLI et SLV forment chacune un motif U-turn, ce qui facilite l’appariement W-C intermoléculaire. Plusieurs autres interactions ont été définies à l’interface I/V, notamment des triplets de bases, ainsi que des empilements de bases. Ces interactions contribuent d’ailleurs à la création d’une structure présentant un empilement continu, c’est-à-dire qui se propage du centre de l’interaction jusqu’aux bouts des tiges de SLI et SLV. Ces études de RMN permettent donc de mieux comprendre la stabilité exceptionnelle de l’interaction kissing-loop I/V au niveau structural et mènent à l’élaboration d’un modèle cinétique de l’activation du substrat par le ribozyme VS. En considérant l’ensemble des données d’ITC et de RMN, l’étonnante stabilité de l’interaction I/V s’explique probablement par une combinaison de facteurs, dont les motifs U-turn, la présence d’un nucléotide exclu de la boucle de SLV (U700), la liaison de cations magnésium et l’empilement de bases continu à la jonction I/V. / Kissing loops are tertiary structure elements that often play key roles in functional RNAs. Their formation is central to many RNA-mediated processes, such as translation initiation, antisense recognition and retroviral dimerization. Kissing loops are also involved in RNA folding as they form long-range interactions between different RNAs or remote domains within the same RNA and stabilize the complex architecture of functional RNA, such as tRNA, riboswitch aptamers and ribozymes. Like several other functional RNAs, the Neurospora VS ribozyme contains an important kissing-loop interaction. The substrate recognition by the VS ribozyme depends largely on the formation of a magnesium-dependent kissing-loop interaction between stem-loop V (SLV) of the catalytic domain and stem-loop I (SLI) that defines the substrate domain. It has been shown from biochemical studies that the I/V kissing-loop interaction involves three Watson-Crick base pairs and is associated with a structural rearrangement of the SLI substrate from an unshifted and inactive to a shifted and active conformation. Here, we present a thermodynamic and structural characterization of the VS ribozyme I/V kissing-loop interaction using isolated stem-loop fragments (SLI and SLV). Both isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR) spectroscopy studies were conducted with several SLI/SLV complexes using a common SLV, but either shiftable or preshifted SLI variants. From the ITC studies, we show that, under saturating amount of magnesium ions, the affinity of the preshifted SLI variants for SLV is remarkably high, the interaction being more stable than predicted for a comparable duplex. In addition, these ITC studies demonstrate that preshifted SLI variants have higher affinity for SLV than shiftable SLI variants, and these results allow us to evaluate the energetic cost of the conformational shift in SLI. From the NMR studies, we confirm formation of three Watson-Crick base pairs at the kissing-loop junction and provide direct evidence on the structural rearrangement of shiftable SLI variants in the presence of magnesium and SLV. The NMR structure of a high-affinity SLI/SLV complex demonstrates that both the SLI and SLV loops adopt U-turn structures, which facilitate intermolecular Watson-Crick base pairing. Several other interactions at the I/V interface, including base triples and base stacking help create a continuously stacked structure. These NMR studies provide a structural basis for the high stability of the kissing-loop interaction and lead us to propose a kinetic model for substrate activation by the VS ribozyme. Taken together, our ITC and NMR data suggest that the remarkable stability of the I/V interaction is likely provided by a combination of several elements, especially the presence of the U-turn motif, the presence of an extruded nucleotide in SLV (U700), the binding of magnesium ions and the extensive base stacking interactions at the junction.

Le ribozyme VS de Neurospora catalyse des réactions de clivage et de ligation d’un lien phosphodiester spécifique essentielles à son cycle de réplication. Il est formé de six régions hélicales (I à VI), qui se divisent en deux domaines, soit le substrat (SLI) et le domaine catalytique (tiges II à VI). Ce dernier comprend deux jonctions à trois voies qui permettent de reconnaître le substrat en tige-boucle de façon spécifique. Ce mode de reconnaissance unique pourrait être exploité pour cibler des ARN repliés pour diverses applications. Bien que le ribozyme VS ait été caractérisé biochimiquement de façon exhaustive, aucune structure à haute résolution du ribozyme complet n’a encore été publiée, ce qui limite la compréhension des mécanismes inhérents à son fonctionnement. Précédemment, une approche de divide-and-conquer a été initiée afin d’étudier la structure des sous-domaines importants du ribozyme VS par spectroscopie de résonance magnétique nucléaire (RMN) mais doit être complétée. Dans le cadre de cette thèse, les structures de la boucle A730 et des jonctions III-IV-V et II-III-VI ont été déterminées par spectroscopie RMN hétéronucléaire. De plus, une approche de spectroscopie RMN a été développée pour la localisation des ions divalents, tandis que diverses approches de marquage isotopique ont été implémentées pour l’étude d’ARN de plus grandes tailles. Les structures RMN de la boucle A730 et des deux jonctions à trois voies révèlent que ces sous-domaines sont bien définis, qu’ils sont formés de plusieurs éléments structuraux récurrents (U-turn, S-turn, triplets de bases et empilement coaxial) et qu’ils contiennent plusieurs sites de liaison de métaux. En outre, un modèle du site actif du ribozyme VS a été construit sur la base des similarités identifiées entre les sites actifs des ribozymes VS et hairpin. Dans l’ensemble, ces études contribuent de façon significative à la compréhension de l’architecture globale du ribozyme VS. De plus, elles permettront de construire un modèle à haute résolution du ribozyme VS tout en favorisant de futures études d’ingénierie. / The Neurospora VS ribozyme catalyzes the cleavage and the ligation of a specific phosphodiester bond, which is essential for its replication cycle. It is formed of six helical regions (I to VI) that are divided in two domains: the substrate (SLI) and the catalytic domain (stems II-VI). The latter contains two three-way junctions that allow recognition of the stem-loop substrate in a specific manner. This unique mode of substrate recognition could be exploited to target folded RNAs for diverse applications. Even though the VS ribozyme has been extensively characterized biochemically, no high-resolution structure of the complete ribozyme has been published yet and this limits our mechanistic understanding. A divide-and-conquer approach was previously initiated to study the structure of the important subdomains of the VS ribozyme by nuclear magnetic resonance (NMR), but this approach needs to be completed. In this thesis, the structures of the A730 loop, the III-IV-V junction and the II-III-VI junction were determined by heteronuclear NMR spectroscopy. Moreover, a unique NMR approach was developed for localizing divalent metal ions, whereas several isotope-labeling strategies were implemented to facilitate the study or large RNA molecules. The NMR structures of the A730 loop and the two three-way junctions reveal that these subdomains are well defined, that they are formed by several recurrent structural elements (U-turn and S-turn motifs, base triples and coaxial stacking) and that they contain several metal-binding sites. Interestingly, structural similarities were identified between the VS and hairpin ribozymes, which allowed the modeling of the VS ribozyme active site. In summary, these studies significantly contribute to a better understanding of the global architecture of the VS ribozyme. In addition, they will allow the construction of a high-resolution model of the complete VS ribozyme and facilitate future engineering studies.

The work presented in this thesis has two parts. The first part deals with methodological developments in the area of solid-state NMR, relevant to the study of partially ordered systems. Liquid crystals are best examples of such partially ordered systems and they are easily oriented by the magnetic field used for the NMR study. They provide spectra rich in information useful for the study of structure and dynamic s of the oriented molecule. Dipolar couplings and anisotropic chemical shifts are relatively easy to obtain for these systems. However, the methodologies used for extracting the required information are constantly undergoing change, with newer ideas being used for optimal use of the technique and increasing the sensitivity of the methodology. In this thesis, existing methods used for obtaining dipolar couplings from oriented liquid crystalline samples are examined in detail and conditions for optimal use of the methods are investigated. Different approaches for enhancing the sensitivity of the techniques are also proposed. Estimation of chemical shift anisotropy of carbons for a molecule that is used as a building block for several mesogens has been obtained and its utility for estimating the order parameters of the system have been examined. The second part of the thesis deals with the application of solid state NMR methods to the study of a number of novel liquid crystalline systems and for the estimation of dynamics, order and orientation of the mesogenic molecules in the magnetic field. Chapter-2 deals with a detailed and systematic study to improve the sensitivity of cross-polarization based separated local field (SLF) NMR spectroscopy techniques such as PISEMA(Polarization Inversion Spin Exchange at the Magic Angle) and PDLF(Pro-ton Detected Local Field). The chapter has been further divided into three sections. Section-A describes the optimization procedure for cross-polarization period for reducing zero-frequency peaks in SLF experiments. Polarization Inversion(PI) is one of the important components of PISEMA and plays a crucial role in enhancing the dipolar cross-peaks and suppressing the axial-peaks. Shortening this period has the advantage of less r.f. power input into the system, thus less susceptibility to sample heating. Therefore it is crucial to arrive at the optimum condition for which maximum sensitivity and resolution are obtained. A detailed experimental investigation of the role of the initial po1arization period has been carried out for two different samples of static oriented liquid crystalline material at two different temperatures and a contact time of 2ms has been found to be optimal for such samples. Insection-B of this chapter, the initial preparation period of the experiment is considered as a possible means of increasing the sensitivity of the experiment. Thus the use of cross-polarization via the dipolar bath by the use of a diabatic demagnetization in the rotating frame(ADRF-CP) has been proposed to be incorporated into PISEMA. To understand the CP dynamics, magnetization in double-and zero-quantum reservoirs of an ensemble of spin-1/2 nuclei and their role in determining the sensitivity the experiments have been theoretically examined. Experimentally, a modification incorporating ADRF-CP is shown to result in enhancement of signal-to-noise by as much as 90% in the case of rigid single crystals of a model peptide and up to 50% in non-rigid, partially ordered liquid crystalline systems. In section-C another useful SLF technique known as PDLF spectroscopy has also been examined. In this case a sweep of one of the r.f. amplitudes(RAMP-CP),rather than ADRF is found to work well. The reason for the different behaviours has been discussed. Chapter-3 highlights two experimental approaches used to extract the chemical shift anisotropy(CSA) tensor information from rotating solids. Section-A is devoted to the measurement of the CSA values of thiophene by using MAS side band analysis, by extracting the principal values from the intensities of just a few spinning side bands. Experiments have been performed on thiophene-2 carboxylic acid and thiophene-3 carboxylic acid samples and the carbon CSA values have been obtained. In section-B, CSA values of carbons of the core unit of the liquid crystal4- hexyloxybenzoic acid (HBA) have been obtained by using the recoupling pulse sequence SUPER(Separation of Undistorted Powder patterns by Effortless Recoupling).HBA belongs to an important class of thermotropic liquid crystals which are structurally simple and often used as starting materials for many novel mesogens. As this molecule could serve as an ideal model compound, high resolution13C NMR studies of HBA in solution, solid and liquid crystalline phases have been also undertaken. The CSA values obtained from the 2D SUPER experiment showed good agreement to those computed by DFT calculations. The CSA values were used for obtaining the order parameter of the system at different temperatures. These matched well the order parameter obtained from the 13C-1 H dipolar couplings in the nematic phase determined by SLF spectroscopy at various temperatures. A knowledge of the CSA of the carbons is thus very useful, as they can be used for gaining knowledge about the system from the chemical shifts obtained from a simple 1D spectrum. In chapter-4, 1-and 2-dimensional13CNMR techniques have been utilized to obtain extensive information about some novel mesogenic molecules. Four molecules of different structure and topology have been taken up for study. These molecules have the following features. Mesogen-1 has a terminal hydroxyl group. Such systems with further modification can result in mesogenic monomers for side chain liquid crystalline polymers. Mesogen-2 has a dimethyl amino group at one end and has three phenyl groups connected by appropriate linking units that form the core. In the third case, mesogen-3, the terminal hydroxyl group of mesogen-1 is replaced with a hydrogen such that13C-1 H dipolar couplings provide directly information on molecular ordering and orientation. In the fourth case, mesogen-4, the core is built with four phenyl rings. Here the fourth ring is linked to other three rings via a flexible chain unit. In each of these cases the 2DSLFNMR experiments have been carried out where13C-1 H dipolar couplings as well as13C chemical shifts were used for obtaining the order parameters of various segments of the molecule. The data provide useful insight into the phase behaviour, ordering and orientation of the molecules. Chapter-5 discusses the applications of the natural abundance 13CNMR techniques to thiophene based mesogens, that have the potential for use in molecular electronics material. Typically, these molecules consist of phenyl rings appropriately connected by linking units with thiophene. Different core units as well as different linking units to thiophene have been considered. The six mesogens thus obtained have been investigated in detail using 1D and 2D NMR methods.13C-1 H dipolar couplings have been used to obtain ordering information, that show interesting correlation to the molecular orientation and dynamics.

Spin selective MQ-SQ correlation has been demonstrated by either selective pulses in homo-nuclear spin systems in isotropic and weakly orienting chiral media or by nonselective pulses in hetero-nuclear spin systems in strongly aligned media. As a consequence of the spin selective correlation, the coherence transfer pathway from MQ to SQ is spin state selective. This two dimensional approach enables the utilization of the passive couplings (remote couplings) to break a complex one dimensional spectrum into many sub spectra. Each sub spectrum contains fewer transitions and hence fewer couplings (active couplings). The role of the passive couplings is to displace the sub spectra and measurement of the displacements taking into account their relative tilt provides the magnitude of the passive couplings along with relative signs. Further possibility of a spin state selective MQ-SQ resolved experiment to determine very small remote couplings otherwise buried within linewidth in one dimensional spectrum has been demonstrated. The resolution of the multiple quantum spectrum in indirect dimension has also been exploited to separate the sub spectra. The technique renders the analysis of complex spectrum in isotropic system much simpler. The potentialities of the technique have also been demonstrated for discrimination of optical enantiomers and derivation of the residual dipolar couplings from very complicated spectrum. The second order spectrum in strongly aligned media restrict selective excitation, however in hetero-nuclear spin system the nonselective pulses on protons do not interact with the hetero-nuclear spins. Thus the weakly coupled part of a strongly coupled spectrum has been exploited for simplifying the second order spectrum and thereby its analysis. Thus several methodologies derived from spin selective correlation has been demonstrated. Enantiopure spectrum has been recorded from a mixture of R and S enantiomers by a novel pulse scheme called Double Quantum Selective Refocusing Experiment. The dipolar coupled methyl protons in weakly orienting media are utilized. The selective excitation of double quantum coherence reduces the three spin system into a two spin system and remote couplings are refocused which otherwise leads to broadening. The sum of passive couplings being different for the enantiomers resolution in the DQ dimension is enhanced and thereby their discrimination. Finally several decoupling schemes has been compared in the indirect dimension of HSQC experiment to resolve 13C satellite spectra otherwise buried within line width for increased confidence in determining hetero-nuclear framework information.

This thesis describes the synthesis and characterisation of titania photocatalysts for incorporation into a polyethylene film. Monodisperse, anatase-phase titania nanoparticles are prepared and the synthesis conditions necessary for attraction to a laponite clay support are determined. Methods of preventing agglomeration of the laponite system such as the use of a polyethylene oxide surfactant or chemical modification of the laponite plate edges with a dimethyloctyl methoxysilane are also explored. Finally, photocatalytic studies on the laponite-supported titania nanoparticles are performed, and the compatibility and photoactivity of these materials in the polyethylene film are examined.