Orientadores: Sérgio Roberto Peres Line, Marcelo Rocha Marques / Texto em português e inglês / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba / Made available in DSpace on 2018-08-24T17:45:16Z (GMT). No. of bitstreams: 1 Ribeiro_MarianaMartins_D.pdf: 2903322 bytes, checksum: 9e0e5e91a22262495ca9bf8ae1d84cec (MD5) Previous issue date: 2014 / Resumo: G-Quadruplexes são estruturas secundárias presentes nas moléculas de DNA e RNA, os quais são formados pelo empilhamento de G-quartetos (interação de quatro guaninas (G-tratos) delimitadas por ligações de hidrogênio do tipo Hoogsteen. O intron 1 do gene PAX9 humano tem um G-quadruplex formado na região localizada perto do exon 1, que é conservada entre os mamíferos placentários. Análises de Dicroísmo Circular (CD), e CD melting mostraram que estas sequências são capazes de formar estruturas quadruplex altamente estáveis. Devido à proximidade da estrutura quadruplex ao limite éxon-íntron foi utilizado um ensaio validado de splicing duplo repórter e PCR em tempo real para analisar o seu papel na eficiência de splicing. O quadruplex humano mostrou ter um papel chave na eficiência de splicing do íntron 1 do gene PAX9, já que uma mutação que aboliu a formação do quadruplex diminuiu drasticamente a eficiência de splicing. O quadruplex de rato, menos estável, mostrou menor eficiência quando comparado com sequências humanas. Além disso, o tratamento com 360A, um forte ligante que estabiliza estruturas quadruplex, aumentou ainda mais a eficiência de splicing do íntron 1 do PAX9 humano. Em conjunto estes resultados fornecem evidências de que as estruturas de G-quadruplex estão envolvidas na eficiência de splicing do intron 1 do gene PAX9 / Abstract: G-Quadruplex are secondary structures present in DNA and RNA molecules, which are formed by stacking of G-quartets (i.e. interaction of four guanines (G-tracts) bounded by Hoogsteen hydrogen bonding). Human PAX9 intron 1 has a putative G-quadruplex- forming region located near exon 1, which is conserved among placental mammals. Using Circular Dichroism (CD) analysis, and CD melting we showed that this region is able to form highly stable quadruplex structures. Due to the proximity of the quadruplex structure to exon-intron boundary we used a validated double reporter splicing assay and real time PCR to analyze its role on splicing efficiency. The human quadruplex was shown to have a key role on splicing efficiency of PAX9 intron 1, as a mutation that abolished quadruplex formation decreased dramatically splicing efficiency. The less stable, rat quadruplex had a less efficient splicing when comparing to human sequences. Additionally, the treatment with 360A, a strong ligand that stabilizes quadruplex structures, further increased splicing efficiency of human PAX9 intron 1. Altogether these results provide evidences that G-quadruplex structures are involved in splicing efficiency of PAX9 intron 1 / Doutorado / Histologia e Embriologia / Doutora em Biologia Buco-Dental

Les séquences d’ADN et d'ARN riches en Guanines peuvent adopter des conformations inhabituelles connues sous le nom de G-quadruplexes (G4). Les topologies et les formes de ces structures fascinantes sont très diverses. Les G4 sont stabilisés par la présence de cations monovalents et des liaisons Hydrogène de type Hoogsteen. De petites molécules contribuent également à la formation de formes stables, principalement par des interactions d'empilement π - π. Bien que les G4 soient connus depuis des décennies, l'intérêt de la communauté scientifique a été stimulé par la découverte de leur effet potentiellement inhibiteur sur la télomérase, une transcriptase inverse impliquée dans la transformation maligne de la plupart des cellules cancéreuses. En ce qui concerne la télomérase, le cancer et G4, plusieurs groupes ont été impliqués dans la découverte de nouveaux stabilisateurs G4 qui peuvent indirectement inhiber l'enzyme. Des centaines de ligands ont été identifiés par ce biais au cours de la dernière décennie et c'est encore un domaine très actif. Prenant en compte les avantages et la facilité qu'offre l'identification de nouvelles structures à l'aide de techniques de calcul grâce à des modèles mathématiques simples et reproductibles, nous avons entrepris un criblage à haut débit et à faible coût de calcul afin d’identifier de nouveaux ligands G4. Avec l'utilisation de la modélisation QSAR nous pouvons prédire l’IC50 d'un ensemble de composés congénères. Nous avons également été en mesure de relier les descripteurs moléculaires qui apparaissent dans nos modèles avec des caractéristiques structurales que les études de la littérature scientifique et SAR ont rapportés dans les études précédentes, pour un ensemble de ligands congénères. En outre, nous avons construit des modèles différents utilisant des ensembles non congénères de composés en appliquant une stratégie de consensus et pu identifier six ligands approuvés par la FDA qui stabilisent les structures G4. Par la suite, en appliquant des techniques non linéaires et un processus pour le traitement de la base de données que nous avons contruite à partir de publications antérieures, nous avons effectué un criblage virtuel de plus de 500 000 ligands d'une base de données commerciale de composés. Nous avons pu identifier de nouveaux ligands avec une puissance plus forte que les précédentes, qui peuvent également stabiliser d’autres structures G4 impliqués dans les processus liés au cancer. Ces observations ouvrent un spectre large de possibilités à explorer. Malgré les limites des techniques de modélisation QSAR explorées tout au long de ce travail, nous considérons qu'elles peuvent être combinées et utilisées avec soin pour répondre à la recherche de nouveaux stabilisateurs G4. / DNA and RNA G-rich sequences can adopt unusual arrangements that are known as G-quadruplexes (G4). The topologies and forms of these fascinating structures are very diverse. G4 are stabilized by the presence of monovalent cations and Hoogsteen Hydrogen bonds. Small molecules also contribute to the formation of stable forms mainly via π-π stacking interactions. Although G4s are known for decades, interest in this field started with their potential effect on inhibition of telomerase enzyme, a Reverse Transcriptase involved in the malignant transformation of most cancer cells. With regards to telomerase, cancer and G4, several groups have been involved in the discovery of new G4 stabilizers that would indirectly inhibit the enzyme. Most of the G4 ligands were identified following this paradigm. Hundreds of ligands have been identified during the past decade and this is still a very active field in science. Taking into account the advantages and easiness that offers the identification of new structures using computational techniques we built single and reproducible mathematical models with high screening capacity and low computational cost in order to use them on the identification of G4 ligands. With the use of QSAR modelling we can predict the telIC50 of a congeneric set of compounds. We have also been able to relate the molecular descriptors that appear in ours models with some structural features that scientific literature and SAR studies have reported in previous studies as appropriated for describing the above mentioned activity, also for congeneric set of ligands. Moreover, we built different models using non congeneric sets of compounds applying a consensus strategy and could identify six FDA approved ligands that stabilize G4 structures. Subsequently, by applying nonlinear techniques and a process for the cure of the database proposed for us in previous publications, we have performed a virtual screening of more than 500 000 ligands from a commercial database of compounds, followed of structure-based model in order to reduce the number of candidates. We were able to identify new ligands with stronger potency than the previous ones, which can also stabilize other G4 structures involved in processes related to cancer. These observations open a wide-ranging spectrum of possibilities to be explored. Despite the limitations of the QSAR modelling techniques explored along this work, we consider they can be combined and used carefully to address the search for new G4 stabilizers.

L’objectif de ces travaux de thèse était l’étude des interactions de petites molécules avec les multiples structures de l’ADN quadruplex via i) le développement et l’utilisation d’un test haut-débit pour l’analyse des interactions ligand-ADN quadruplex et le criblage de chimiothèques/ciblothèques et ii) la préparation de composés aux modes d’interactions multiples (empilement/sillon, covalent/non-covalent, etc.), sélectifs (quadruplex vs. duplex et intra-quadruplex) et éventuellement fonctionnalisés (biotine, fluorophore, etc.). La première partie des travaux a été centrée sur le développement du test G4-FID (G-quadruplex Fluorescent Intercalator Displacement) qui est une méthode semi-quantitative permettant l’évaluation de l’affinité et de la sélectivité de petites molécules pour l’ADN quadruplex par déplacement d’une sonde off/on, le Thiazole Orange (TO). Le test a notamment été transposé avec succès de la cuve vers la microplaque (HT-G4-FID). D’autre part, nous avons montré l’intérêt de fluorophores alternatifs, TO-PRO-3 et Hoechst 33258, aux caractéristiques spectrales complémentaires à TO. Cette méthode d’analyse a également été utilisée avec succès pour l’identification de nouveaux ligands sélectifs d’ADN quadruplex et la mise en évidence des relations structure-activité ainsi que des sélectivités structurales. La deuxième partie des travaux a été consacrée à la préparation et à l’étude de nouveaux ligands d’ADN quadruplex. Ces ligands possèdent des particularités, soit dans leur mode d’interaction (sillons, coordination) soit par leur bifonctionnalité (biotinylés, fluorescents). Nous avons ainsi préparé un ligand de quadruplex polyhétéroaryle acyclique (TOxaPy) possédant une sélectivité inattendue pour certaines structures de l’ADN quadruplex. D’autre part, nous avons montré que les complexes de dérivés de terpyridine peuvent être adaptés, en changeant le ligand organique et/ou la nature du métal, de façon à interagir avec l’ADN quadruplex par interaction covalentes et/ou non covalentes. / The aim of this thesis work was to study the interactions of small molecules with multiple structures of quadruplex DNA via i) the development and use of a high-throughput test for the analysis of ligand-quadruplex DNA interactions and screening of chemical libraries and ii) the preparation of compounds with multiple binding modes (stacking/groove, covalent/non-covalent, etc..) selective (quadruplex vs. duplex and intra-quadruplex) and possibly functionalized (biotin, fluorophore, etc.). The first part of the work was focused on the development of the G4-FID (G-quadruplex Intercalator Fluorescent Displacement) assay, which is a semi-quantitative method for evaluating the affinity and selectivity of small molecules for quadruplex DNA by displacing an off/on probe, the Thiazole Orange (TO). The test has been implemented successfully with microplate (HT-G4-FID). On the other hand, we have shown the importance of alternative fluorophores, TO-PRO-3 and Hoechst 33258, with complementary spectral characteristics. This method of analysis has also been successfully used for the identification of new selective ligands of quadruplex DNA and the identification of structure-activity relationships and structural selectivities. The second part of the work was devoted to the preparation and study of new DNA quadruplex ligands. These ligands possess particular characteristics either in their mode of interaction (grooves, coordination) or by their bifunctionality (biotinylated, fluorescent). We have prepared an acyclic polyheteroaryle quadruplex ligand (TOxaPy) with an unexpected selectivity for certain structures of quadruplex DNA. Furthermore, we showed that complexes of terpyridine derivatives can be tailored by changing the organic ligand and / or the metal in order to interact with quadruplex DNA by covalent and / or non-covalent interaction.

Les quadruplexes de guanines (G4) sont des structures non canoniques d'acides nucléiques formées par des séquences d'ADN ou d'ARN contenant des blocs de guanines. In vivo, ces structures pourraient être impliquées de façon transitoire dans de nombreux processus cellulaires, en particulier au niveau des télomères. Dans ce dernier cas, la formation de G4 aux télomères au moyen de ligands favorisant ces structures pourrait limiter la prolifération de cellules tumorales. Au cours de ce travail de thèse, nous avons développé une méthode de criblage à moyen débit permettant de tester l'effet de diverses molécules sur la stabilisation du G4 télomérique humain. Cette méthode, basée sur la dénaturation thermique de G4 suivie en fluorescence, en présence d'autres structures compétitrices d'ADN, a permis d'identifier plusieurs familles de ligands présentant des affinités et des sélectivités intéressantes, tels que des dérivés macrocycliques de néomycine et des N-méthylbisquinolinium phénanthrolines. Nous avons ensuite caractérisé plus précisément les mécanismes moléculaires expliquant la stabilisation des G4 par divers ligands. L'étude cinétique sur un modèle de G4 tétramoléculaire a permis de mettre en évidence la possibilité d'une accélération importante de la vitesse d'association des G4 par certaines familles de composés. Nous avons également analysé l'inhibition de la télomérase en présence de ces ligands. En utilisant un test d'extension d'amorce par la télomérase, nous avons montré que seuls certains ligands étaient capables d'enrayer l'élongation par la télomérase sur un substrat ne formant pas initialement de G4 intramoléculaire. Ces résultats appuient l'hypothèse selon laquelle les effets cellulaires de ces ligands ne sont pas uniquement corrélés à leur effet sur la télomérase, mais aussi à des effets connexes impliquant d'autres protéines télomériques, essentielles au maintien de télomères fonctionnels. Enfin, nous avons transposé cette stratégie de ciblage du télomère pour limiter la prolifération cellulaire, à l'agent pathogène responsable de la Malaria : Plasmodium falciparum. Nous avons montré l'existence d'une extrémité télomérique 3' sortante chez le parasite et son potentiel repliement en G4 dans des conditions physiologiques. Plusieurs molécules stabilisant les G4 télomériques du parasite avec une bonne sélectivité ont été identifiées, et leur impact sur sa prolifération a été testé.

Les télomères sont des structures nucléoprotéiques nécessaires à la protection des extrémités des chromosomes contre les dégradations ou fusions induites par les processus de réparation de lADN. Ils sont constitués de complexes protéiques associés à des répétitions en tandem dun motif 5-(TTAGGG)-3 sous forme double brin de plusieurs kilobases, et finalisés par une extrémité 3simple brin de la même séquence de quelques centaines de bases. On observe in vitro un raccourcissement des télomères à chaque division cellulaire, ce même fait est corrélé in vivo avec le vieillissement. Lorsque les télomères se raccourcissent et atteignent une taille critique, les cellules entrent en sénescence réplicative qui se définit par un arrêt de croissance définitif et viable des cellules. La télomérase est une ADN polymerase ARN-dépendante qui allonge le télomère en lui ajoutant des séquences répétitives TTAGGG. Elle comprend une composante ARN (hTR) qui sert de matrice et une composante catalytique à activité transcriptase inverse (hTERT). Lexpression seule dhTERT suffit à immortaliser différents types cellulaires. La télomérase est fortement exprimée dans la majorité des cellules tumorales alors que son activité est difficilement détectable dans la plupart des cellules somatiques. Ces observations font de la télomérase une cible dintérêt pour des nouvelles thérapies anticancéreuses. Une de ces nouvelles stratégies consiste en lutilisation de molécules capables de stabiliser les structures en G-quadruplexe de lADN. La stabilisation des G-quadruplexes télomériques rend les télomères inaccessibles pour la télomérase et inhibe son activité par la séquestration de son substrat. Lobjectif de cette thèse est dévaluer la réponse cellulaire induite par le traitement cellulaire de deux ligands des G-quadruplexes au niveau du protéome des cellules WI38 transfectées pour exprimer hTERT. Les deux ligands, TMPyP4 et la télomestatine, inhibent la télomérase mais ont une spécificité différente pour les diverses structures G-quadruplexes. En premier lieu, nous avons étudié leffet de la transfection dhTERT sur des cellules fibroblastiques humaines (WI38). Cette première étude a été conduite afin de caractériser ladaptation cellulaire résultante de limmortalisation des cellules WI38. Par la suite, celle-ci permettra de comparer ces résultats avec ceux obtenus lors de létude protéomique de leffet des ligands des G-quadruplexes. Nous avons montré que hTERT induit une augmentation de la capacité fonctionnelle du réticulum endoplasmique ainsi quune modulation des signaux cellulaire Ca2+-dépendant. Nous proposons que cette adaptation cellulaire est responsable dune résistance accrue vis-à-vis de différents stress environnementaux. Dautres protéines impliquées dans des mécanismes doncogenèse ont été identifiées et sont différentiellement exprimées entre les cellules parentales et les cellules transfectées. Lanalyse protéomique des traitements cellulaires indique que TMPyP4 induit une altération du protéome beaucoup plus prononcée que celle induite par la télomestatine. Ceci est probablement dû au manque de spécificité de TMPyP4 pour les G-quadruplexes télomériques. TMPyP4 induit, entre autres, une sous-expression massive des hnRNPs, une modulation de la voie protéasomale, une diminution probable de la traduction et une surexpression de plusieurs chaperonnes moléculaires. La télomestatine induit notamment une surexpression de la protéine BCL2A1 qui est impliquée dans les processus de résistance aux agents anticancéreux et une probable augmentation de la traduction. Les deux ligands ont des effets communs sur la variation dexpression des chaperons CCT (sou-expression), de lHSP90 alpha (surexpression) et de lhnRNP D (sous-expression). LHSP90 est également surexprimée dans les cellules hTERT-WI38 par rapport aux cellules parentales. Cette protéine fait actuellement lobjet de nombreuses recherches visant à inhiber son activité du fait de son implication en oncogenèse ainsi que dans la modulation de lactivité de la télomérase. Enfin, nous avons montré lintérêt de ce type détude protéomique dans lévaluation dagents à vocation thérapeutique préalablement aux études cliniques.

Depuis plusieurs années, on observe un intérêt grandissant envers des structures particulières de l’ADN, les quadruplexes de guanine ou G4. Ces structures, largement étudiées in vitro, sont encore peu connues in cellulo mais semblent jouer un rôle important dans la régulation de l’expression génétique. Elles ont rapidement été considérées comme des cibles thérapeutiques potentielles pour certaines maladies telles que le cancer. Le premier indice de leur existence dans les cellules n’a été obtenu qu’en 2013 par immunodétection sur des cellules fixées. Les recherches sont actuellement tournées vers le développement de nouveaux outils moléculaires qui permettraient la visualisation des G4 dans des cellules vivantes.C’est dans ce cadre que nous avons imaginé une série de complexes polyazaaromatiques de ruthéniumII à base de ligands plans étendus (heptacycle dpqp et octacycle dppqp). La combinaison des propriétés photophysiques des complexes de RuII associées à la présence d’un large plan étendu supposé interagir avec les G4, fait de ces molécules des outils potentiels pour l’étude des G4 in cellulo.La première partie de ce projet porte sur la synthèse de ces nouveaux complexes de ruthénium. Une méthode originale de "chimie sur complexe" a permis d'obtenir, entre autres, un complexe possédant le ligand dpqp, fonctionnalisé par une triple liaison. Il a également été possible, par « chimie sur complexe », de construire un cycle supplémentaire sur le ligand heptacyclique (dpqp) chélaté pour obtenir les complexes [Ru(L)2dppqp]2+. Les propriétés photophysiques des différents complexes ont été étudiées. Seuls deux complexes, [Ru(phen)2dpqp-Cl]2+ et [Ru(TAP)2dpqp-Cl]2+, présentent un comportement s’approchant de celui des complexes de référence; c’est à dire des rendements quantiques comparables à [Ru(bpy)3]2+ et des durées de vie de l’état excité de l’ordre de la centaine de nanosecondes. Les autres complexes sont non luminescents et l’hypothèse d’un quenching par transfert de proton à l’état excité a été avancée pour expliquer ce comportement.Les complexes ont aussi été évalués vis à vis de différentes structures oligonucléotidiques G4 et duplexes. Tous les complexes possèdent une affinité correcte envers les G4. Comme nous l'espérions, le complexe porteur du ligand octacyclique semble être particulièrement sélectif envers les G4 par rapport à l'ADN double brin. Il a aussi été montré que deux des complexes testés ont le potentiel d'être utilisés comme sondes moléculaires "light-switch ON" pour les structures G4 en milieu cellulaire. Certains des complexes synthétisés possèdent donc le potentiel pour devenir de bons outils moléculaires pour l’étude des G4 in cellulo. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The subject of this diploma thesis is the influence of selected chemicals on cell lines viability. The theoretical part contains options of cancer treatment by using chemotherapeutics including their mechanism of action and side effects. Additionally, there are described alternative DNA structures with focus on G-quadruplexes and ligands that interact with G-quadruplexes. These compounds are promising drugs in cancer treatment due to their high specificity to G-quadruplexes, which are found in telomeres of chromosomes. G-quadruplex interacting ligands by stabilization of G-quadruplexes can inhibit the enzyme telomerase, which is necessary for telomere lengthening of rapidly dividing cancer cells. Additionally, the possibilities of viability assays are summarized in the theoretical part. The aim of the experimental part was comparing cytotoxic activity between commercially available chemotherapeutics and selected G-quadruplex interacting ligands. Another task was the study of apoptosis and necrosis after the treatment of selected chemicals on cell lines and after the localization of ligands interacting with G-quadruplexes in the cells of the breast cancer cell line. In the experimental part, G-quadruplex interacting ligands have been shown to exhibit similar cytotoxic activity to commercially available chemotherapeutic agents.

ATRX is a chromatin remodeling protein associated with X-linked Alpha-Thalassemia Mental Retardation syndrome and cancers that use the Alternative Lengthening of Telomere pathway. In the absence of ATRX there is a DNA damage response associated with telomeres and the expression of certain genes are perturbed. Recent findings (Law et al, 2010 Cell) have shown that ATRX is preferentially enriched at GC-rich tandem repeats in the genome. The mechanism for this localisation is unknown but may be related to the potential for these GC-rich tandem repeats to adopt non-B form DNA structures; ATRX has been shown to bind such structures (G4) in vitro. This study aims to understand the specific factors of the repeats that signal ATRX targeting. To address the research questions, an experimental system was developed, in which known targets, the ψζ VNTR and telomere repeats, were inserted into an inducible ectopic gene in the 293T-Rex cell line by site-directed recombination. ATRX was found to be enriched at the ectopic repeats compared to an endogenous negative control suggesting that it is recruited by the repeats independent of its original context. Furthermore, ATRX enrichment increased upon transcription of the ectopic gene, and this was dependent on the orientation of the repeat with the non-template strand being G-rich. Interestingly, when the repeat was transcribed, the distribution of ATRX across the repeats was asymmetrical with most ATRX binding downstream of the repeat. Moreover, there was a direct correlation between the repeat size and level of ATRX bound: the longer the repeat the higher the increase in ATRX enrichment. To determine the signal for ATRX binding, assays were performed to look for features which reflected the distribution of ATRX including H3K9me3, RNA polII, G4, R loops and DNA supercoiling. R loops look to be a strong candidate for the signaling of ATRX binding.

Meiotic recombination is a prerequisite for exchange of genetic information in all Sexually reproducing organisms. This process is initiated by the formation of double stranded breaks (DSBs) in DNA followed by homology directed repair. The process is subjected to surveillance mechanisms that control DSB formation and allow for repair of DSBs by halting cell cycle progression. Interestingly, though generation of DSBs is an Essential event in meiosis they are nevertheless regarded as the most lethal forms of DNA damage. If left unrepaired a single DSB can lead to gene deletion, duplication, translocations and missegregation of large chromosome fragments leading to cell death. In Saccharomyces cerevisiae, genetic screens for mutants defective in meiotic recombination led to the identification of a group of genes called the RAD52 epistasis group which includes RAD50, RAD51, RAD52, RAD54, RAD55, RAD57, RAD59, MRE11 and XRS2. A subset of these genes, namely MRE11, RAD50 and XRS2, have been shown by genetic studies to be essential for several nuclear events including sensing DSBs, double strand break repair (DSBR) by homologous recombination (HR) and non homologous end joining (NHEJ), telomere length maintenance, cell cycle activation in response to DSBs, mitotic and meiotic recombination. In vitro, Mre11 displays Mn2+-dependent endonuclease activity on ssDNA, 3'-5' Exonuclease on single- and double-stranded DNA, strand annealing and weak hairpin Opening activities. Mutational analyses have revealed two functional domains in Mre11- Then terminal nuclease domain involved in telomere length maintenance and DSB Processing and the C terminal DNA binding domain involved in DSB formation during Meiosis. Rad50, a 153 kDa protein shares homology with the SMC (Structural Maintenance of Chromosome) family of proteins which are involved in chromosome Condensation and cohesion. It consists of a bipartite N- and C terminal Walker A and Walker B motifs separated by a heptad repeat sequence which folds into an antiparallel Coiled-coil structure. The heptad repeats are separated by a metal binding globular region the Zn hook. Rad50 is an ATP-dependent DNA-binding protein. hRad50 regulates the exonuclease activity of hMre11. Unlike Mre11 and Rad50, which are evolutionarily conserved, Xrs2 is found only in S. cerevisiae and Nbs1 in mammals. Xrs2 appears to be sequence non-specific DNA- binding protein. Xrs2 in yeast or Nbs1 is its counterpart in mammals target Mre11 and Rad50 to the sites of DNA damage and mediate S-phase cell cycle checkpoint activation. Mutations in either one of the MRX subunits results in defects in repair of DSBs, activation of cell cycle checkpoint and shortened telomeres leading to genomic instability. Hypomorphic mutations in MRE11 and NBS1 lead to genetic disorders- A-TLD (ataxia-telangiectasia-like disorder) and NBS (Nijmegen breakage syndrome) respectively, that are phenotypic ally related to AT (ataxia-telangiectasia) caused by mutations in ATM. Patients with AT, A-TLD or NBS syndromes are hypersensitive to radiomimetic agents and are predisposed to cancer. Several lines of evidence suggest that S. cerevisiae strains bearing mre11Δ, rad50Δ or xrs2Δ display shortening of telomeres. Telomeres are the nucleoprotein ends of all linear eukaryotic chromosomes that are important in maintaining the integrity of the genome.Telomeres are comprised of repetitive G rich sequence most of which is double stranded but the extreme 3' end protrudes to form 3' single stranded overhang called the G tail. elopers are essential in preventing end-end fusion of chromosome, are important for chromosome replication, segregation and genome stability. Genetic studies have implicated the MRX complex in both telomerase-dependent and independent telomere length maintenance. Studies have indicated a direct role for S. cerevisiae MRE11 in the proper establishment of telomere end-structure. However, the molecular mechanism of MRX at telomeres is poorly understood. To understand the role(s) of MRX complex at telomeres, it is important to elucidate the biochemical activities of MRX complex as well as its individual subunits on the telomere DNA structures. Since, Mre11 complex is known to function in several processes related to DNA metabolism it becomes imperative to study the function of Mre11 complex on DNA substrates in the context of a given nuclear process. The 3' single trended telomeric sequence is capable of acquiring folded conformation(s) as a mechanism of end protection which is mediated by several telomere-specific and nonspecific ending proteins. In mammals, the 3' ssDNA has been demonstrated to fold into tloop configuration mediated by some of the components of sheltrin protein complex, wherein the ssDNA invades the duplex DNA resulting in the formation of a displacement loop (D loop). Evidence for the formation of t-loop has been shown in vitro with human telomeres. However, the formation of t-loops has not been demonstrated in S. cerevisiae. Nevertheless, there is growing body of evidence which suggests the formation of alternative DNA structures such as G4 DNA at the yeast telomeres. G quadruplexes (G quartets or G4 DNA) are thermodynamically stable structures formed by Hoogsteen base pairing between guanine residues. In a G quartet the four guanine residues are paired, where each guanine residue is an electron acceptor and a donor and stabilized by a metal cation. The presence of G rich motifs at the promoter regions, rDNA, telomeres and recombination hot spots indicate that G4 DNA has important functions in vivo. Although the existence of G4 DNA has been the subject of much debate, the identification of several proteins that promote (Rap1, Hop1, Topo I, TEBPβ), modify and resolve (POT1, TERT, KEM1, GQN1, BLM, WRN, Rte1) G4 DNA, together with the direct visualization of G4 DNA using G4 DNA specific antibodies and RNA interference have provided compelling for the existence of G4 DNA in vivo. To elucidate the function of MRX complex or its individual subunits at telomeres, the biochemical activities of purified MRX complex and its individual subunits on G4 DNA, D loop, duplex DNA and G rich ssDNA has been analyzed in this study. G4 DNA was assembled from S. cerevisiae telomeric sequence. G4 DNA was isolated and its identity was ascertained by chemical probing and circular dichroism. S. cerevisiae MRE11 and XRS2 was cloned and expressed in E. coli BL21 (DE3)plysS. S. cerevisiae RAD50 in pPM231 vector in S. cerevisiae BJ5464 strain was a gift from Dr. Patrick Sung (Yale University). Mre11, Rad50 and Xrs2 were overexpressed and purified to >98% homogeneity. The identity of the proteins was ascertained by Western bloting using polyclonal antibodies. Using purified proteins heterotrimeric MRX and heterodimeric MR and MX protein complexes were formed in the absence of ATP, DNA or Mn2+. The ability of M/R/X to bind to telomeric DNA substrates was studied by electrophoretic mobility shift assays. Mre11, Rad50, Xrs2 and MRX displayed higher binding affinity for G4 DNA over D loop, ss- or dsDNA. MRX bound G4 DNA more efficiently compared to its individual subunits as 10-fold lower concentration of MRX was able to shift the DNA into the protein-DNA complex. The protein-G4 DNA complexes were stable as >0.8 M NaCl as required to dissociate 50% of protein-G4 DNA complexes. Efficient competition by poly(dG), which is known to fold into G4 DNA, suggested that the protein-G4 DNA complex was specific. Competition experiments with tetra-[N-methyl- pyridyl]-porphyrin suggested that M/R/X recognizes distinct determinants and makes specific interactions with G4 DNA. G4 DNA is highly polymorphic and can exist as intramolecular or intermolecular (parallel and antiparallel) structures. High affinity binding of Mre11 to G4 DNA (parallel) over G2' DNA (antiparallel), ss- and dsDNA suggests the existence of parallel G4 DNA structures at the telomeres and that G4 DNA may be the natural substrate for MRX complex in vivo. Telomeres are elongated by telomerase that requires access to the 3' G-tail for its activity. Formation of G4 DNA structures renders the 3' G-tail inaccessible to telomerase thereby inhibiting telomere elongation. To elucidate the functional relevance of high affinity of M/R/X for G4 DNA, the ability of the complex to generate the appropriate DNA structure for telomere elongation has been analyzed. In this study, I considered the possibility that MRX could act as: (a) a helicase that opens up the G4 DNA structures making it accessible to telomerase or (b) as a nuclease that cleaves the G4 DNA generating substrates for telomerase. Helicase assay with Mre11, Xrs2, MX and MRX on G4 DNA and duplex DNA showed no detectable DNA unwinding activity. Interestingly, nuclease assays with Mre11 on G4 DNA showed that Mre11 cleaved G4 DNA in Mn2+-dependent manner and the cleavage was mapped to the G residues at the stacks of G quartets. Mre11 cleaved telomeric duplex DNA in the center of TGTG repeat sequence, G rich ssDNA at 5' G residue in an array of 3 G residues and D loop structure preferentially at the 5' ends at TG residues. Significantly, the endonuclease activity of Mre11 was abrogated by Rad50. Xrs2 had no effect on the endonuclease activity of Mre11. Structural studies on Rad50 and Mre11 showed that binding of ATP by Rad50 positions the Rad50 catalytic domain in close proximity to the nuclease active site of Mre11. In yeast, disruption of ATP binding Walker motifs results in a null phenotype, suggesting that ATP is required for Rad50 functions in vivo. hRad50 is known to regulate the exonuclease activity of hMre11 in the presence of ATP. Therefore, can ATP modulate the effect of S. cerevisiae (Sc) Rad50 on ScMre11? To address this question, I monitored the ATPase activity of Rad50 in the absence or presence of DNA. Rad50 hydrolyzed ATP in a DNA-independent manner; however, ATPase activity was enhanced in the presence of Mre11 and Xrs2. However, Rad50 exhibited a low turnover indicating that ATP could function as a switch molecule. Based on these observations, the effect of ATP on the nuclease activity was examined. The binding of ATP and its hydrolysis by Rad50 attenuated the inhibition exerted by Rad50 on the Mre11 endonuclease activity. Cleavage of G4 DNA, D loop, duplex DNA and ssDNA required ATP hydrolysis, since no cleavage product was observed when ADP or ATPγS was substituted for ATP. This observation was corroborated using a hairpin DNA substrate that mimics a intermediate in VDJ recombination, thereby confirming the generality of regulation of Rad50 on the endonuclease activity of Mre11. Does Rad50 regulate the exonuclease activity of Mre11 as well? To address this question, exonuclease activity of Mre11, MR and MRX on 3' labeled duplex DNA and G4 DNA was assayed. Rad50 had no measurable effect on the exonuclease activity of Mre11. Based on previous studies and my observations, I propose a model for the role of MRX in telomere length maintenance and its regulation by the ATP-binding pocket of Rad50. MRX binds telomeric DNA substrates in a non-productive complex, which is converted to a catalytically active complex upon binding of ATP by Rad50. ATP induces conformational changes, repositioning the complex such that the catalytic site of Mre11 now has access to the substrate. Following cleavage of DNA by Mre11, the release of ADP and inorganic phosphate, generate the cleaved product. The cleaved DNA is now accessible to telomerase or telomere binding proteins. In summary, the data presented in my PhD thesis demonstrates that Mre11 is a structure- and sequence-specific endonuclease. The natural substrate for telomerase is the 3' ssDNA. G quartets at telomeres not only protect the ends from degradation but also make the ends inaccessible for telomerase activity. Genetic studies have shown that cells proficient for telomerase activity but lacking any one of the components of the MRX complex display shortening in telomere length. The ability of Mre11 to cleave G4 DNA at the stacks of G quartets therefore, suggests a mechanism by which the 3' ssDNA is rendered accessible to telomerase or other telomere binding proteins. Yeast telomeres are characterized by the presence of subtelomeric Y' elements proximal to the terminal TG1- 3 repeat sequences. The Y' element has been shown to be amplified by telomerase in a fraction of mutants with short telomeres. The mechanism by which Y' DNA is amplified is unclear. The ability of Mre11 to cleave telomere duplex DNA at the center of TGTG repeats could contribute to the generation of appropriate substrate for elongation by telomerase, thereby contributing to Y' DNA amplification. Telomere length is maintained by homeostasis between processes that contribute to telomere elongation and those that cause attrition in telomeric ends. Overelongated telomeres are brought to wild type telomere size by a unique recombinational single step deletion process termed telomere rapid deletion (TRD). TRD involves invasion of the elongated 3' G tail into the proximal telomeric tract resulting in the formation of the D loop structure. Following branch migration the D-loop is nicked and resolved into a deleted telomere and a circular liner product. Cells deleted for MRE11, RAD50 or XRS2 are deficient in TRD process. It has been hypothesized that Mre11 could be a candidate for cleaving the D-loop structure. The endonuclease activity of Mre11 on D-loop structure, preferentially at the 5' ends at TG residues demonstrated in this study, show that Mre11 could function as the nuclease required to generate the deleted telomere in TRD. MRX complex is involved in several processes involving DNA metabolism. It is important that the activities of the complex are regulated in the in vivo context. Complex formation and the interaction of the individual subunits with nucleotide cofactors and metal ions constitute a mode of regulation. This study shows that Rad50 regulates the endonuclease, but not exonuclease activity of Mre11. The binding of ATP and its hydrolysis by Rad50 brings in the regulatory factor necessary to keep the uncontrolled nuclease activity of MRX in check, thus preventing any deleterious effects on telomere length. Telomere maintenance by telomerase is activated in 80% of cancer cells. Inhibition of telomerase by G quartets provides a new drug targets for potential anti-cancer drugs. It is, therefore, likely that understanding the biological consequences of G quadruplex interactions would provide a better insight in development of therapeutics for cancer.

15N-based nuclear magnetic resonance techniques are considered very powerful to study the molecular properties of platinum-containing anticancer agents, these properties being responsible for the efficacy of the compounds, but also for the understanding of resistance mechanisms and toxicity. Therefore, the first part of the present work aimed to develop a new method for synthesizing 15N-labeled, chiral platinum compounds. A theoretical discussion on the nucleophilic ring-opening of aziridines has also been envisaged, rationalizing an interesting regiochemistry question. Indeed, a surprising inversion of regiochemistry arose during the development of the above-mentioned synthetic pathway, and density functional theory calculation brought a rational framework to the experimental findings.<p><p>Infrared spectroscopy probes the global chemical composition of a sample and has been used to produce a snapshot of cancer cells contents after treatment with platinum coordinates. Indeed, in vitro studies focused here on the use of modern spectroscopic methods to fingerprint the cellular impact of platinum complexes. These drug signatures help to classify and select promising compounds. It makes no doubt that such systemic approaches for compound discovery are helpful technologies. Also, we made the use of the COMPARE algorithm from the NCI, which analyzes similarity between any active compounds previously tested by the NCI large scale in vitro screening program of anticancer agents. <p><p>The last chapter aimed to study the interactions between a series of platinum coordinates and DNA. Binding mode to telomeric-like sequences and binding kinetics to genomic-like sequences were assessed to investigate any differences between the compounds and to gain insight into structure-activity relationships. <p> / Doctorat en Sciences biomédicales et pharmaceutiques / info:eu-repo/semantics/nonPublished