In recent years, there has been an increasing demand for newer, more accurate, technologies that can detect and identify biomolecules or biological entities related to health, agriculture or the environment. With the discovery of new properties of nucleic acids beyond the storage and transfer of genetic information, a new class of nucleic acid-based biosensors is emerging, using DNA and RNA as target recognition elements with the advantage of being simpler and more cost-effective compared to antibodies-based biosensor. Two sequences, TrG14MC and TrG10SC, with evidence to suggest that they are capable of inhibit the metalloenzyme CIP, were isolated from a selection conducted by Dr. Razvan Nutiu. Here we study the inhibitory properties of these two aptamer candidates and measure the IC50 value, determined as 94 nM for TrG14MC and 83 nM for TrG10SC. Different bivalent constructs, designed to increase the inhibitory effect of the isolated sequences, are studied showing a pronounce influence of the linker length improving the inhibitory effect over CIP. Modulating the interaction of the isolated sequences and the CIP is of key importance in order to develop a successful biosensor. Therefore, we try to recover CIP from the inhibition effect by using antisense sequences complementary to different segments of the construct. The maximum recovery, 75%, was achieved by an antisense sequence fully complemented to the inhibitory bivalent construct. We also study here the use of a linker in the bivalent construct that forms a secondary hairpin structure, and the effect of linearizing that structure with an antisense sequence complementary to the linker. This resulted in as 12% of the inhibitory effect. The purpose of this investigation was to establish the first steps toward the development of a new class of biosensors capable of disinhibiting CIP upon the recognition of a specific target, taking advantage of the suggested CIP-inhibitory properties of the isolated sequences TrG14MC and TrG10SC. / Thesis / Master of Applied Science (MASc)

Vários estudos têm apontado a sinalização e os receptores purinérgicos, representados em mamíferos pelos receptores ionotrópicos (P2X1 P2X7) e metabotrópicos (P2Y1,2,4,6, 11,12,14), como um sistema primitivo, envolvido não somente na sinalização neuronal, mas também em muitos outros processos vitais incluindo resposta imune, inflamação, dor, agregação plaquetária e nos processos de diferenciação, proliferação e morte celular, que ocorrem no desenvolvimento e na regeneração tecidual. Condizente com as descrições da literatura, dados do nosso laboratório, baseados na farmacologia dos receptores purinérgicos, sugeriram o envolvimento do subtipo P2Y2 na proliferação e na neurogênese in vitro de células de carcinoma embrionário P19. Tendo em vista a ausência de agonistas e antagonistas específicos para a maioria dos subtipos de receptores purinérgicos, o que vem dificultando a elucidação das funções exatas desses receptores em processos fisiológicos e patológicos, optamos para o screening de uma biblioteca combinatória de oligonucleotídeos para a identificação de ligantes de alta afinidade e especificidade para o receptor P2Y2 (procedimento de SELEX, Evolução Sistemática de Ligantes por Enriquecimento Exponencial). Essa abordagem envolve passos reiterativos de seleção in vitro de moléculas de RNA, estabilizadas por substituição do grupo 2´OH das pirimidinas por um átomo de flúor, que possuem afinidade pelo receptor, até que a mistura de RNAs, originalmente de 1013 diferentes seqüências que adotam uma gama de estruturas secundárias e terciárias, esteja purificada para uma população homogênea de ligantes de alta afinidade pelo receptor P2Y2. O processo envolve a transcrição in vitro da biblioteca de DNA para RNA, a apresentação desta ao alvo, a eluição dos ligantes específicos, denominados aptâmeros, e a regeneração da biblioteca de DNA por RT-PCR, a qual, após uma reação de transcrição in vitro, gera a mistura de RNAs para o próximo ciclo de seleção. Neste trabalho, nós utilizamos como alvo o receptor P2Y2 recombinante humano expresso na linhagem de células de astroglioma humano 1321N1. Ao final de nove ciclos de SELEX, nós isolamos 46 sequências que foram agrupadas em três classes estruturais, de acordo com a presença de regiões consensos. A mistura destas moléculas se ligou ao receptor P2Y2 humano com uma constante de dissociação de 164 nM. Um dos clones isolados, o aptâmero B7, se ligou preferencialmente ao receptor P2Y2 (Kd 184 nM), em relação aos receptores P2Y1 e P2Y4 recombinantes expressos em células 1321N1. A interação deste aptâmero não foi dependente da espécie, uma vez que ele foi capaz de se ligar tanto ao receptor P2Y2 de origem humana como murina. A atividade biológica do aptâmero foi avaliada em células P19 (sabidamente expressando receptores P2Y2 endógenos), na qual a proteção do ATP contra a apoptose, provavelmente interagindo com o receptor P2Y2, foi anulada na presença deste aptâmero em uma concentração mil vezes menor do que a do ATP. Além de confirmar a viabilidade da técnica SELEX para identificar ligantes subtipos-específicos dos receptores purinérgicos, o aptâmero anti-P2Y2 serve como ferramenta fundamental para definir demais funções fisiológicas deste receptor. Passos de otimização das suas propriedades como ligante e biodisponibilidade tornarão este aptâmero um composto de alta relevância farmacêutica. / Many published studies have focused on purinergic signaling and receptors, represented by ionotropic (P2X1 P2X7) and metabotropic (P2Y1,2,4,6,11,12,14) subtypes as a universal system which is not only involved in neuronal signaling, but also in various other vital processes including immune response, inflammation, platelet aggregation as well as differentiation, proliferation and cell death occurring during development and tissue regeneration. In agreement with other published reports, results of our laboratory based on overlapping purinergic receptor pharmacology suggest the participation of the P2Y2 subtype in proliferation and in vitro neurogenesis of P19 embryonal carcinoma cells. In view of the lack of availability of specific agonists and antagonists for most purinergic receptors making the elucidation of exact functions of these receptors in their cellular context almost impossible, we used a combinatorial oligonucleotide library approach, denominated SELEX (Systematic Evolution of Ligands by Exponential Enrichment) for the development of high-affinity and specificity ligands for the P2Y2 receptor. This approach is based on re-iterative steps of in vitro selection of 2´-fluoro-pyrimidine-modified RNA molecules for receptor-binding affinity from an RNA pool containing 1013 different sequences and secondary and tertiary structures until this pool is purified to a homogeneous population of ligands with high affinity to the P2Y2 receptor. The combinatorial DNA library is in vitro transcribed into RNA followed by target presentation of the RNA library and elution of the target-binders, denominated aptamers, and RT-PCR amplification in order to restore the DNA library used for in vitro transcription for next SELEX cycle. Following nine SELEX cycles using 1321N1 human astroglial cells expressing recombinant human P2Y2 receptors as target, we isolated 46 aptamer sequences which, based on consensus sequence motifs, were grouped in three structural groups. The mixture of the isolated sequences bound themselves to human P2Y2 receptors with a dissociation constant (Kd) of 164 nM. One of the isolated clones, the aptamer denominated B7, bound itself to P2Y2 receptors in preference to P2Y1 and P2Y4 recombinant receptors expressed in 1321N1 cells. The binding activity of the aptamer was not limited to P2Y2 receptors of human origin, as the aptamer also interacted with mouse P2Y2 receptors. The capability of the aptamer of affecting the biological activity of P2Y2 receptors was verified in P19 cells in which ATP-induced protection against apoptosis, mediated by P2Y2 receptors, was abolished in the presence of the aptamer. In addition to providing a proof of principle for the feasibility of developing purinergic subtype-specific ligands by using the SELEX technique, the anti-P2Y aptamer provides a fundamental tool for gaining insights of physiological functions of this receptor in various cellular contexts. Moreover, steps of optimization of receptor binding properties and aptamer half-life in vivo will turn this aptamer into a compound of high pharmaceutical relevance.

A galectina-1 (Gal1) é uma lectina, altamente conservada, que reconhece ?- galactosídeos, e está envolvida na regulação da tolerância da imunidade celular e na homeostase. Dados da literatura mostram que esta lectina endógena é amplamente expressa em locais de inflamação e na tumorigênese, participando diretamente dos processos de adesão celular, crescimento tumoral, metástase e angiogênese, ressaltando a relevância de sua detecção em amostras biológicas, e sugerindo que a inibição dirigida da Gal1 pode resultar em benefícios no tratamento de distúrbios inflamatórios e em novas estratégias terapêuticas antitumorais. Entretanto, ainda são escassos os dados sobre inibidores de Gal1 com real impacto terapêutico no bloqueio da atividade biológica dessa lectina. Os aptâmeros são oligonucleotídeos de cadeia simples (DNA ou RNA), que podem se ligar a uma vasta diversidade de alvos, tais como íons, peptídeos, proteínas, moléculas orgânicas e inorgânicas, com alta afinidade e especificidade. Os aptâmeros são selecionados a partir de bibliotecas com sequências randômicas de oligonucleotídeos fita simples (ssDNA) constituídos por uma região central variável, flanqueada por duas regiões de interação com primers para amplificação das sequências via PCR. Esse processo de seleção é denominado de Evolução Sistemática de Ligantes por Enriquecimento Exponencial (SELEX). Neste trabalho foram selecionados e caracterizados aptâmeros de DNA que se ligam a Gal1 humana recombinante e inibem sua atividade lectínica. O processo de seleção dos aptâmeros foi feito através de uma variação da metodologia SELEX, desenvolvida neste trabalho e aqui denominada de \"single vial selection\" (SVS), na qual todas as etapas de seleção dos aptâmeros ocorreram em um único recipiente, de forma rápida e eficiente, evitando etapas cromatográficas, que geralmente são utilizadas no SELEX. Análises com a técnica de termoflúor (TSA) e espectroscopia de fluorescência intrínseca do triptofano permitiram confirmar que os aptâmeros, de fato, se ligam a Gal1, mas em um sítio afastado do CRD. Ensaios de hemaglutinação mostraram que os aptâmeros selecionados conseguiram inibir a ligação da Gal1 com as glicanas da superfície celular, bloqueando a atividade lectínica da proteína. Assim, esse conjunto de resultados mostram que foi possível o desenvolvimento de uma nova classe de inibidores da Gal1 baseada em aptâmeros de DNA, a partir de uma nova metodologia de SELEX, e que não atuam através dos mecanismos clássicos de bloqueio da atividade lectínica via CRD, abrindo nossas possibilidades no desenvolvimento de estratégias diagnósticas e terapêuticas envolvendo esta proteína. / Galectin-1 (Gal1) is a highly conserved lectin that recognizes ?-galactosides, involved in the regulation of cellular immunity tolerance and homeostasis. Data from the literature show that this endogenous lectin is widely expressed in sites of inflammation and tumorigenesis, directly participating in cell adhesion processes, tumor growth, metastasis and angiogenesis, highlighting the relevance of its detection in biological samples, and suggesting that its direct inhibition may result in benefits in the treatment of inflammatory disorders and in novel antitumor therapeutic strategies. However, data on Gal1 inhibitors with real therapeutic impact in blocking the biological activity of this lectin are still scarce. Aptamers are single-stranded oligonucleotides (DNA or RNA), which can bind to a wide variety of targets, such as ions, peptides, proteins, organic and inorganic molecules, with high affinity and specificity. The aptamers are selected from pools of random single-stranded oligonucleotide (ssDNA) sequences consisting of a variable central region, flanked by two sites of primers interaction for PCR amplification. This selection process is called Systematic Evolution of Ligands by EXponential enrichment (SELEX). In this work, DNA aptamers that bind to recombinant human Gal1 and inhibit their lectin activity have been selected and characterized. The aptamers selection process was done through a variation of SELEX methodology, developed in this work and here called \"single vial selection\" (SVS), in which all stages of aptamers selection occurred in a single container, quickly and efficient, avoiding chromatographic steps, which are usually used in SELEX. Analyzes by Thermofluor (TSA) method and intrinsic tryptophan fluorescence spectroscopy have confirmed that aptamers actually bind to Gal1, but at a site away from the CRD. Hemagglutination assay showed that selected aptamers succeeded in inhibiting the Gal1 binding to cell surface glycans, blocking the protein lectin activity. Thus, this set of results showed that it was possible to develop a new class of Gal1 inhibitors based on DNA aptamers and on a new SELEX methodology, that does not act through the classic blocking mechanisms of lectin activity via CRD, opening new possibilities for the development of diagnostic and therapeutic strategies involving this protein.

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No. of bitstreams: 2 Dissertação - Amanda Gabrielle da Silva - 2015.pdf: 1218291 bytes, checksum: 56dd4b22c77bb02a83c9d20a4cc4e0ce (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2015-09-09 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / Considering potential molecular methods for diagnostic and/or therapeutic purpose of infectious human diseases, such as dengue, highlights the systematic evolution of ligands by exponential enrichment, known as SELEX. In this method, ligands to a target are exponentially enriched generating aptamers of DNA or RNA with high specificity, being considered as artificial antibodies. In this work, we aimed to realize the isolation of aptamers binding to 3'-UTR (untranslated region) of the RNA from dengue virus (DENV), because present important conformational structures that act as functional elements into RNA necessary in the infectious process. Total RNA of C6/36 infected cells was extracted, submitted to reverse transcription reaction to obtain viral cDNA (serotypes 2 and 3) and amplified by symmetric and/or asymmetric PCR technique to produce the 3’-UTR from DENV as target, generating RNA-like by containing deoxyuridine triphosphate (dUTP) and biotin in the 5’ region of the target. The random library of RNA ligands was obtained by sonication of a pool from human genomic DNA used in three successive PCR, and in the last reaction was introduced the promoter of T7 RNA polymerase, presenting fragments ranging from 80 to 600-bp. Eight rounds of selection were performed between the target and the library by using paramagnetic particles coated with streptavidin. For each round, after the incubation, the non-ligands were removed by using magnetic platform, and the ligands were eluted with NaOH. The eluted ligands were precipitated, submitted to RT-PCR and transcription in vitro, completing one round of selection. For analysis of variability of ligands, the product obtained from the eighth round was cloned and fourteen clones were randomly selected for amplification. The results demonstrated that the aptamers presented sizes with estimated molecular weights varying from 80 to 100-bp. These data indicated the viability of aptamers isolation against conformational elements present in the 3'-UTR of RNA from dengue virus, which may contribute to future research focusing on prevention and/or control of the disease. / Dentre os potenciais métodos moleculares para o diagnóstico e/ou terapêutica de doenças que acometem a saúde humana, tais como a dengue, destaca-se a seleção de ligantes pela utilização da química combinatória, conhecida como SELEX. Nesse método, os ligantes a um alvo são enriquecidos exponencialmente tendo como produto final a obtenção de aptâmeros de DNA ou RNA com elevada especificidade, sendo considerados como anticorpos artificiais. No presente trabalho foi realizado o isolamento de aptâmeros de RNA ligantes à extremidade 3’-UTR (untranslated region) do RNA do vírus da dengue (DENV), por apresentar elementos de RNA conformacionais e funcionais importantes no processo infeccioso. A partir do RNA extraído de células C6/36 infectadas foi feita a transcrição reversa (RT) para produção de cDNA viral (sorotipos 2 e 3) e amplificação por PCR simétrica e/ou assimétrica para a produção do alvo 3’-UTR do DENV, na forma de RNA-like por conter desoxiuridina trifosfatada (dUTP) e biotina na extremidade 5’. A biblioteca randômica de ligantes de RNA foi obtida por sonicação de um pool de DNA genômico humano utilizado como alvo em três PCRs sucessivas sendo que na última reação foi introduzido o promotor da T7 RNA polimerase e cujos fragmentos variaram de 80 a 600-pb. Foram realizados oito rounds de seleção entre alvo e biblioteca utilizando partículas paramagnéticas revestidas com estreptavidina. A cada round, após o período de incubação, os oligonucleotideos não ligantes foram removidos com o auxílio de plataforma magnética, e os ligantes foram eluídos com NaOH. Os ligantes eluídos foram precipitados e submetidos à RT-PCR e transcrição in vitro, finalizando um round de seleção. Para verificar a variabilidade de ligantes, o produto do oitavo round foi clonado e 14 clones foram selecionados aleatoriamente para amplificação. Os resultados demonstraram que os aptâmeros isolados possuem tamanhos distintos, com pesos moleculares estimados variando de 80 a 100-pb. Os dados aqui obtidos indicaram a viabilidade do processo de isolamento de aptâmeros para elementos conformacionais presentes na extremidade 3’-UTR do RNA do vírus da dengue os quais poderão contribuir para pesquisas futuras com foco na prevenção e/ou controle da doença.

Vários estudos têm apontado a sinalização e os receptores purinérgicos, representados em mamíferos pelos receptores ionotrópicos (P2X1 P2X7) e metabotrópicos (P2Y1,2,4,6, 11,12,14), como um sistema primitivo, envolvido não somente na sinalização neuronal, mas também em muitos outros processos vitais incluindo resposta imune, inflamação, dor, agregação plaquetária e nos processos de diferenciação, proliferação e morte celular, que ocorrem no desenvolvimento e na regeneração tecidual. Condizente com as descrições da literatura, dados do nosso laboratório, baseados na farmacologia dos receptores purinérgicos, sugeriram o envolvimento do subtipo P2Y2 na proliferação e na neurogênese in vitro de células de carcinoma embrionário P19. Tendo em vista a ausência de agonistas e antagonistas específicos para a maioria dos subtipos de receptores purinérgicos, o que vem dificultando a elucidação das funções exatas desses receptores em processos fisiológicos e patológicos, optamos para o screening de uma biblioteca combinatória de oligonucleotídeos para a identificação de ligantes de alta afinidade e especificidade para o receptor P2Y2 (procedimento de SELEX, Evolução Sistemática de Ligantes por Enriquecimento Exponencial). Essa abordagem envolve passos reiterativos de seleção in vitro de moléculas de RNA, estabilizadas por substituição do grupo 2´OH das pirimidinas por um átomo de flúor, que possuem afinidade pelo receptor, até que a mistura de RNAs, originalmente de 1013 diferentes seqüências que adotam uma gama de estruturas secundárias e terciárias, esteja purificada para uma população homogênea de ligantes de alta afinidade pelo receptor P2Y2. O processo envolve a transcrição in vitro da biblioteca de DNA para RNA, a apresentação desta ao alvo, a eluição dos ligantes específicos, denominados aptâmeros, e a regeneração da biblioteca de DNA por RT-PCR, a qual, após uma reação de transcrição in vitro, gera a mistura de RNAs para o próximo ciclo de seleção. Neste trabalho, nós utilizamos como alvo o receptor P2Y2 recombinante humano expresso na linhagem de células de astroglioma humano 1321N1. Ao final de nove ciclos de SELEX, nós isolamos 46 sequências que foram agrupadas em três classes estruturais, de acordo com a presença de regiões consensos. A mistura destas moléculas se ligou ao receptor P2Y2 humano com uma constante de dissociação de 164 nM. Um dos clones isolados, o aptâmero B7, se ligou preferencialmente ao receptor P2Y2 (Kd 184 nM), em relação aos receptores P2Y1 e P2Y4 recombinantes expressos em células 1321N1. A interação deste aptâmero não foi dependente da espécie, uma vez que ele foi capaz de se ligar tanto ao receptor P2Y2 de origem humana como murina. A atividade biológica do aptâmero foi avaliada em células P19 (sabidamente expressando receptores P2Y2 endógenos), na qual a proteção do ATP contra a apoptose, provavelmente interagindo com o receptor P2Y2, foi anulada na presença deste aptâmero em uma concentração mil vezes menor do que a do ATP. Além de confirmar a viabilidade da técnica SELEX para identificar ligantes subtipos-específicos dos receptores purinérgicos, o aptâmero anti-P2Y2 serve como ferramenta fundamental para definir demais funções fisiológicas deste receptor. Passos de otimização das suas propriedades como ligante e biodisponibilidade tornarão este aptâmero um composto de alta relevância farmacêutica. / Many published studies have focused on purinergic signaling and receptors, represented by ionotropic (P2X1 P2X7) and metabotropic (P2Y1,2,4,6,11,12,14) subtypes as a universal system which is not only involved in neuronal signaling, but also in various other vital processes including immune response, inflammation, platelet aggregation as well as differentiation, proliferation and cell death occurring during development and tissue regeneration. In agreement with other published reports, results of our laboratory based on overlapping purinergic receptor pharmacology suggest the participation of the P2Y2 subtype in proliferation and in vitro neurogenesis of P19 embryonal carcinoma cells. In view of the lack of availability of specific agonists and antagonists for most purinergic receptors making the elucidation of exact functions of these receptors in their cellular context almost impossible, we used a combinatorial oligonucleotide library approach, denominated SELEX (Systematic Evolution of Ligands by Exponential Enrichment) for the development of high-affinity and specificity ligands for the P2Y2 receptor. This approach is based on re-iterative steps of in vitro selection of 2´-fluoro-pyrimidine-modified RNA molecules for receptor-binding affinity from an RNA pool containing 1013 different sequences and secondary and tertiary structures until this pool is purified to a homogeneous population of ligands with high affinity to the P2Y2 receptor. The combinatorial DNA library is in vitro transcribed into RNA followed by target presentation of the RNA library and elution of the target-binders, denominated aptamers, and RT-PCR amplification in order to restore the DNA library used for in vitro transcription for next SELEX cycle. Following nine SELEX cycles using 1321N1 human astroglial cells expressing recombinant human P2Y2 receptors as target, we isolated 46 aptamer sequences which, based on consensus sequence motifs, were grouped in three structural groups. The mixture of the isolated sequences bound themselves to human P2Y2 receptors with a dissociation constant (Kd) of 164 nM. One of the isolated clones, the aptamer denominated B7, bound itself to P2Y2 receptors in preference to P2Y1 and P2Y4 recombinant receptors expressed in 1321N1 cells. The binding activity of the aptamer was not limited to P2Y2 receptors of human origin, as the aptamer also interacted with mouse P2Y2 receptors. The capability of the aptamer of affecting the biological activity of P2Y2 receptors was verified in P19 cells in which ATP-induced protection against apoptosis, mediated by P2Y2 receptors, was abolished in the presence of the aptamer. In addition to providing a proof of principle for the feasibility of developing purinergic subtype-specific ligands by using the SELEX technique, the anti-P2Y aptamer provides a fundamental tool for gaining insights of physiological functions of this receptor in various cellular contexts. Moreover, steps of optimization of receptor binding properties and aptamer half-life in vivo will turn this aptamer into a compound of high pharmaceutical relevance.

Les ribozymes sont des ARN naturels ou artificiels possédant une activité catalytique. Les ribozymes artificiels ont été identifiés in vitro par la méthode SELEX, et plusieurs d'entre eux ont été caractérisés par des études cinétiques. Ces molécules sont impliquées dans des réactions de clivage, de ligation, de modification d'extrémités d'ARN, de polymérisation, de phosphorylation et d'activation de groupements acyl. Parce qu'elle est nécessaire à la traduction, l'aminoacylation des ARN joue un rôle évolutif important dans la transition du monde de l'ARN vers le monde moderne de l'ADN et des protéines, et elle est centrale à l'établissement du code génétique. Plusieurs ribozymes catalysant le transfert d'acides aminés à partir de cofacteurs activants ont pu être isolés et caractérisés depuis une vingtaine d'années, ce qui a documenté la possibilité d'aminoacylation d'ARNt en l'absence des aminoacyl ARNt synthétases. En développant un nouveau protocole SELEX basé sur l'oxydation au périodate, le but de notre travail est de découvrir de nouveau ribozymes d'une taille de l'ordre d'une vingtaine de nucléotides pouvant combiner la catalyse de l'activation des acides aminé et la transestérification. Bien que des molécules catalysant l'une ou l'autre des deux réactions ont été identifiées, aucun ribozyme n'existe à ce jour qui puisse utiliser des acides aminés libres et un cofacteur activant pour réaliser l'aminoacylation en 3' dans un même milieu réactionnel. La sélection de molécules actives dans une approche SELEX exige la présence de régions constantes sur les deux extrémités des séquences pools aléatoires initiaux. Ces régions sont nécessaires pour l'amplification par PCR, mais elles imposent des contraintes importantes pour l'identification de ribozymes car elles peuvent complètement inhiber leur activité par interférence structurelle. Nous présentons un protocole optimisé qui minimise la taille de ces régions constantes. D'autre part, notre nouveau design est très spécifique pour la sélection d'ARN aminoacylés sur l'extrémité 3'. Ce protocole a été utilisé pour réaliser 6 à 7 cycles de sélection avec différents pools, et un enrichissement en séquences spécifiques a pu être mis en évidence. Bien que certains tests avec les pools sélectionnés a révélé une activité possible, des essais avec des séquences spécifiques de ces pools n'ont pour l'instant pas pu confirmer l'activité catalytique recherchée. Un protocole basé sur le même principe de sélection a été utilisé dans une étude parallèle pour identifier les ARN aminoacylés présents dans l'ARN total d'Escherichia coli. Dans ce deuxième travail, note but est d'identifier tous les d'ARN aminoacylés par séquençage massif, avec à la clé la découverte possible de molécules autres que les ARNt et ARNtm. En utilisant les ARNt comme modèle, nous nous sommes aperçus qu'un protocole RNAseq standard n'était pas adapté à cause des bases modifiées présentes sur ces molécules. Nous avons développé et mis au point un nouveau protocole pour l'identification de n'importe quelle séquence aminoacylée en 3'. La nouvelle approche présentée devrait permette l'étude exhaustive de l'aminoacylation de toutes les séquences présentes dans l'ARN total. / Ribozymes are natural or in vitro selected RNA molecules possessing a catalytic activity. Artificial ribozymes have been extensively investigated by in vitro SELEX experiments, and characterized by kinetic assays. Ribozymes are involved in RNA cleavage, ligation, capping, polymerization, phosphorylation and acyl activation. Because it is required for translation, RNA aminoacylation plays an important role in the evolution from the late RNA world to the modern DNA and protein world, and is central to the genetic code. Several ribozymes catalyzing amino acid transfer from various activating groups have already been selected and characterized in the past two decades, documenting the possibility of tRNA aminoacylation in the absence of aminoacyl tRNA synthetase. With a newly designed SELEX protocol based on periodate oxydation, the aim of our investigation is to uncover small ribozymes of the order of 20 nucleotides that could catalyze both amino acid activation and transesterification. Although molecules catalyzing either reaction have been identified, no existing ribozyme could use free amino acids and activating cofactor(s) as substrates for 3' esterification in a single reactional context. The selection of active molecules in a SELEX procedure requires the presence of constant tracks on both ends of the sequences constituting the initial random pools. These tracks are required for PCR amplification, but they impose significant burden to the identification of ribozymes because they can prevent any activity through structural inhibition. We present an optimized protocol that significantly minimizes the size of these constant tracks. At the same time, our newly design protocol is very specific for the selection of 3'-end aminoacylated RNA. Working with this protocol, we performed 6 to 7 cycles of selection with different pools, and observed an enrichement with specific sequences. Although some experiments performed with entire pools did reveal a possible activity, no activity could be so far confirmed with specific sequences. A similar protocol was also applied in a parallel study to identify aminoacylated RNA from total RNA in Escherichia coli. In this other approach, our goal is to possibly identify new classes of aminoacylated RNA while using the deep sequencing technology. Using tRNA to validate our protocol, we realized that a standard RNAseq procedure could not work due to the presence of modified bases. We established a new method for bank preparation to identify any sequence aminoacylated at the 3' end. Ultimately, this new approach will allow us to study the level of aminoacylation of any sequence present in total RNA.

Les amplifications de répétitions de triplets CTG dans le gène DMPK humain sont à l'origine de la dystrophie myotonique de type 1 ou DM1. Les répétitions CUG présentes dans les ARNm DMPK séquestrent le facteur d'épissage MBNL1 au sein de foci nucléaires et dérégulent l'épissage des pré-ARNm cibles de MBNL1. Par ailleurs, 9 isoformes de MBNL1, produites par épissage alternative, coexistent dans les cellules. Dans un premier temps nous avons recherché quels exons constitutifs ou alternatifs étaient requis pour la reconnaissance des ARN, la régulation de l'épissage et la localisation cellulaire de MBNL1. Nous avons ensuite entrepris de rechercher par l'approche SELEX les séquences de haute affinité pour MBNL1. Nous avons ainsi identifié une séquence conservée de 12 nucléotides de long, contenant un seul motif de fixation pour MBNL1 et adoptant une structuration tige-boucle particulière. L'importance de cette structuration a été confirmée par l'existence de mutants compensatoires au sein des ARN sélectionnés. Finalement nous avons étudié les mécanismes de régulation de l'inclusion de l'exon 5 du pré-ARNm de la troponine T cardiaque humaine (hcTNT). Une approche in cellulo nous a permis d'identifier les séquences minimales requises pour la régulation de l'épissage en conditions normales et en présence des répétitions CUG. Au sein de ces séquences nous avons identifié 6 nouveaux sites MBNL1 dont nous avons montré l'importance fonctionnelle in cellulo et in vitro. Nous avons également mis en évidence l'implication d'autres séquences régulatrices dans la régulation de l'inclusion de l'exon 5 du pré-ARNm hcTNT et un rôle de la protéine hnRNP H dans ces régulations. L'ensemble de ces données apportent de nouveaux éléments d'information importants pour la compréhension de la DM1 / Amplifications of CTG motifs in the human DMPK gene are responsible for Myotonic Dystrophy of type 1. The resulting CUG repeats in pre-mRNAs capture the MBNL1 splicing factor, leading to mis-regulation of MBNL1 pre-mRNA targets. Due to the recent discovery of MBNL1 and its numerous isoforms (9) resulting from alternative splicing, little is known on how MBNL1 regulates splicing and how a decreased level of available MBNL1 generates splicing miss-regulations. First, we defined which of the MBNL1 alternative and constitutive exons are required for: i) RNA binding, ii) splicing activity and, iii) MBNL1 sub-cellular localization. Second, for a more precise definition of the MBNL1 RNA binding properties, we performed SELEX experiments using a library of RNA stem-loop structures containing a 18-nt long randomized sequence. Its leads to the identification of 12-nt long sequence adopting a peculiar stem-loop structure, whose importance for MBNL1 binding was revealed by its preservation by compensatory base-pair mutations. Finally, based on the above data, we studied the mechanisms involved in regulation of hcTNT exon 5 splicing. By in cellulo assays, we defined the hcTNT pre-mRNA region required for both normal inclusion and for the trans-dominant effect of CUG repeats. Within this region, we identified six new potential MBNL1 sites and demonstrated their functional role by in vitro and in cellulo assays. We also identified several additional splicing regulatory elements involved in normal and CUG-deregulated exon 5 inclusion and already showed a role of hnRNP H in splicing regulation. Altogether, our data bring new information important for understanding the pathology

La protéine MC1 est une petite protéine structurale très abondante chez Methanosarcina thermophila (archaeabactérie). Nous avons utilisé la méthode SELEX (Systematic Evolution of Ligands by EXponential enrichment) pour rechercher ses séquences préférentielles de fixation. Après 10 cycles de sélection, une séquence consensus avec une affinité 50 fois plus forte que celle pour une séquence aléatoire a été déterminée. Cette séquence a été étudiée par simulation de dynamique moléculaire. Le mode de fixation de MC1 sur l?ADN a ensuite été déterminé par des empreintes moléculaires (DMS, OH·). Les résultats montrent une fixation par une face et dans le petit sillon de l?ADN. Une reconnaissance par lecture indirecte des séquences est probable. L?oxydation de certains acides aminés (Trp, Met) par les rayons gamma entraîne une modification des propriétés de la protéine : perte de la reconnaissance de structures et séquences particulières et diminution de sa capacité à courber l?ADN.

This work was designed as a proof-of-principle concept or prototype to show the effect of protein-assisted targeting of DNA to specific genomic loci. Two strategies were employed to deliver the DNA with the aim that once inside the cell the DNA would be delivered to the target sequence by the assistance of a protein. In our case, the chosen protein was the site-specific meganuclease I-SceI. The first strategy described herein was to bind the targeting DNA to I-SceI by the use of a fusion protein between I-SceI and a known DNA-binding domain, the GAL4-DBD. The second strategy involved using a DNA aptamer to I-SceI to link the targeting DNA and I-SceI. Testing in vivo revealed that in our human cells (HEK-293) single-stranded DNA was more efficient at gene targeting than double-stranded DNA. In order for the first strategy to work, we needed to have some region of double-stranded DNA. We found that in human cells, it was better for gene targeting to have that double-stranded DNA on the 5’ side of our targeting DNA. We also used gel shift assays to confirm binding by our candidate DNA-binding domain, the GAL4-DBD. We were unable to detect expression of the fusion protein of I-SceI and the GAL4-DBD. For the second strategy we were able to construct an aptamer to I-SceI using a variant of the systematic evolution of ligands by exponential enrichment (SELEX). The I-SceI aptamer was synthesized as part of a longer DNA molecule containing homology to a target locus. Using this chimeric oligonucleotide (part aptamer, part DNA repair region) testing was done in both yeast and human cells. Aside from instances where the aptamer’s secondary structure may have been compromised, the aptamer containing oligonucleotide stimulated repair at a rate 2 to 15-fold higher than the non-selected control sequence. These experimental results show that by delivering targeting DNA within close proximity to the site of modification, gene targeting frequencies can be increased.

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No. of bitstreams: 2 Dissertação - Elismar de Jesus Nunes Cnossen - 2014.pdf: 4126749 bytes, checksum: eacd4dd92411aa26514ec275da57a07e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-01-21 / Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG / The increasing number of notifications of dengue infections is becoming a very important concern for global healthcare programs. Combinatorial technologies aiming the selection of specific short conformational nucleic acid ligands against viral targets, also called aptamers, can be achieved by large-scale selections using the genomic SELEX technology. Our hypothesis is that aptamers can be directly selected against dengue RNA conformational structures that present functional elements in the 5'-UTR sequence, which form RNA-RNA and protein- RNA interactions, and play significant roles in the infection process. Our aim was to select and characterize aptamers that bind to the 5’-UTR using the matrix-free SELEX method. Products from the eighth selection cycle were isolated, cloned and sequenced, and 14 ligands were chosen for in silico characterization. Aptamers were grouped into three families according to their sequence homology, and conserved ribonucleotides generated specific linear motifs. Sequences motifs were detected in random nucleotides regions ranging from 31 to 40 nt, which showed higher affinity to DENV1 and 3 virus. The novel molecules and processes described in this study open new insights for dengue research and applications, and the selected aptamers can be used either as diagnostic or therapeutic tools. In silico analyses revealed that aptamer binding to its RNA target may lead to alterations of viral RNA secondary structures, and is probably leading to the loss of its original conformational and preventing its replication and/or the transcription process. The analyses also demonstrated that aptamers presented a broad hybridization spectrum to DENV1 and 3 even in the presence of mutations in different subtypes, which suggest its possible use in the other two serotypes, DENV2 and 4. This is the first description of aptamers against the RNA structure of Dengue Virus with important implications in the disease control. / O aumento do número de notificações de infecções causadas pela dengue está se tornando uma grande preocupação para os programas globais de saúde. Tecnologias combinatórias destinadas à seleção de ligantes específicos de ácidos nucléicos curtos conformacionais contra alvos virais, também chamados aptâmeros, podem ser conseguidos pelas seleções em larga escala, utilizando a tecnologia do SELEX genômico. Nossa hipótese é que os aptâmeros podem ser selecionados diretamente contra as estruturas conformacionais de RNA da dengue, as quais apresentam elementos funcionais na sequência 5'-UTR, que formam interações RNA-RNA e RNA-proteína, e desempenham papéis importantes no processo de infecção. O nosso objetivo foi selecionar e caracterizar aptâmeros que se ligam a região 5'-UTR utilizando o método matrix-free SELEX . Produtos do oitavo ciclo de seleção foram isolados, clonados e sequenciados, e 14 ligantes foram escolhidos para a caracterização in silico. Os aptâmeros foram agrupados em três famílias de acordo com a homologia das sequências, e ribonucleotídeos conservados geraram motivos lineares específicos. Sequências motivos foram detectadas em regiões aleatórias de nucleotídeos variando de 31-40 nt que apresentaram a maior afinidade para DENV1 e 3. As novas moléculas e processos descritos neste estudo abrem novas perspectivas para a pesquisa e aplicações na dengue, e os aptâmeros selecionados podem ser usados tanto como ferramentas diagnósticas ou terapêuticas. As análises in silico revelaram que a ligação do aptâmeros ao seu alvo de RNA pode levar a alterações na estrutura secundária do RNA viral, e provavelmente levando à perda da sua conformação original e impedindo a sua replicação e/ou o processo de transcrição. As análises também demonstraram que os aptâmeros apresentaram um largo espectro de hibridação ao DENV1 e 3, mesmo na presença de mutações em diferentes subtipos, o que sugere a sua possível utilização nos outros dois sorotipos, DENV2 e 4. Esta é a primeira descrição de aptâmeros contra a estrutura de RNA do Vírus da Dengue com implicações importantes no controle da doença.