The anti-tumor activity of platinum based drugs is mediated by their ability to attack DNA. Platinum complexes can alter the structure of DNA by modifying the bases, mainly guanines. The biological consequnces of such interactions are compromising replication and transcription. RNA polymerase complex can stall at a damaged site in DNA and mark the lesion for repair by proteins that are utilized to execute nucleotide excision repair, a pathway commonly associated with the removal of bulky DNA damage from the genome. This RNA polymerase-induced repair pathway is called transcription-coupled nucleotide excision repair. Main goal of this thesis was to study RNA polymerases tolerance of DNA damage by novel, biologically active platinum (II) complexes involving derivatives of aromatic cytokinines as the ligands; cis-[Pt(2-chloro-6-(4-methoxybenzylamino)-9-isopropylpurin)2Cl2](PR-001), cis-[Pt(2-chloro-6-(benzylamino)-9-isopropylpurin)2Cl2](PR-002 )and cis-[Pt(2-(3-hydroxypropylamino)-6-(benzylamino)-9-isopropylpurin)2Cl2](PR-005). DNA templates (constructs) that contain a single, site-specific DNA lesion and support transcription by human RNA polymerase II and bacteriophage T7 RNA polymerase were prepared. The method is making use of polymerase chain reaction (PCR) and biotin-streptavidin interactions and paramagnetic particles to purify the final product. Synthetic oligomers duplexes (75-mer, 56-mer and 15-mer) are ligated to 5´-biotin pCI-neo-G-lessT7 PCR fragment, the 15-mer is either unmodified or modified with a site-specific lesion of PR-005 and cisplatin. We also studied the inhibition of RNA polymerases activity on globally modified plasmid pCI-neo and pUC 19 by novel platinum complexes and cisplatin. We found that bifunctional adducts of complex PR-005 contrary to adducts of PR-001 and PR-002 effectively decrease amount of full lenght transcripts produced by both, human and bacterial RNA polymerases. This result can be explained by a sterical block, induced to DNA by intrastrand cross-link of PR-005 with bulky aromatic ligands.

Transcription initiation is a key step at which gene expression can be regulated. The sigma subunit of RNA polymerase provides the enzyme with the ability to recognize promoter sequences and initiate transcription at specific sites on the chromosome. The molecular basis of sigma function is not well known. It has been suggested that sigma factors confer promoter specificty by making direct contacts to the promoter DNA (Losick and Pero, 1981). To test this idea, suppressors of promoter down mutations were sought that affected the promoter recogniton properties of the σ70 subunit of E. coli RNA polymerase. Four such sigma mutants were obtained, two of which are allele-specific. One of these mutants has a change at a position in the predicted helix-turn-helix DNA binding structure which lies in a conserved region of the protein (region 4). This mutant specifically suppresses promoter down mutations in the -35 region of the promoter. The other mutant has a change at a residue that lies in a predicted α-helix of conserved region 2. This mutant specifically suppresses promoter mutations in the -10 region of the promoter. These data support the idea that regions 2 and 4 of sigma interact with the -10 and -35 regions of the promoter, respectively.

In this thesis, I address two fundamental questions related to our understanding of how DNA damage is processed and repaired during replication. Using Two-dimensional (2-D) agarose gel analysis, I first examine whether DNA damage on plasmids introduced by transformation is processed in a manner similar to that observed on endogenously replicating plasmids and the chromosome. The original intent for using this approach was to develop a technique that could examine how different DNA adducts would be repaired in various sequence contexts. However, I found that distinct differences exist between the processing of DNA damage on transforming plasmids and the chromosome. The 2-D agarose gel analysis shows that RecA-mediated processing does not contribute to the survival of transforming plasmids and that this effect is likely due to inefficient replication of the plasmids after they are initially introduced into cells. These observations, while important, place limitations on the usefulness of transforming plasmids to characterize cellular repair processes. In a second question, I characterize the composition of the replisome following arrest by UV-induced DNA damage. Using 2-D agarose gel analysis the structural changes that occur in DNA during processing and repair have been well characterized, however, little is known about the fate of the replisome itself during these events. I used thermosensitive replication mutants to compare the DNA structural intermediates induced after disruption of specific components of the replisome to those observed after UV damage. The results show that dissociation of subunits required for polymerase stabilization are sufficient to induce the same processing events observed after UV damage. By contrast, disruption of the helicase-primase complex induces abnormal structures and a loss of replication integrity, suggesting that these components remain intact and bound to the template following replication arrest. I propose that polymerase dissociation provides a mechanism that allows repair proteins to gain access to the lesion while retention of the helicase serves to maintain the integrity and licensing of the fork so that replication can resume from the appropriate site once the lesion has been processed.

Indiana University-Purdue University Indianapolis (IUPUI) / In an effort to advance the methodology in analyzing RNAPII protein-protein interaction network and to determine the role of the CTD in controlling RNAPII transcription, we devised a method to specifically isolate the CTD-associated and CTD-less RNAPII to identify the proteins that interact with both the CTD and the globular core of RNAPII using novel purification scheme coupled to quantitative proteomics.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Human apurinic/apyrimidinic endonuclease 1 (hApe1) is a multi-functional protein having two major functions: apurinic/apyrimidinic endonuclease activity for DNA damage repair and redox activity for gene regulation. Many studies have shown the action of Ape1 in the base excision repair pathway leading to cell survival. It has also been reported that Ape1 reduces a number of important transcription factors that are involved in cancer promotion and progression. Though the repair activity is well understood, the redox mechanism is not yet clear. What is known about Ape1 is its structure and that it contains seven cysteines (C65, C93, C99, C138, C208, C296, and C310), none of which are disulfide bonded. Two of these cysteines, C99 and C138, are solvent-accessible, and C65, C93, and C99 are located in the redox domain. It is believed that one or more cysteines are involved in the redox function and is hypothesized that hApe1 reduces the down-stream transcription factors by a disulfide exchange mechanism. E3330, (2E)-3-[5-(2,3-dimethoxy-6-methyl-1,4-benzoquninoyl)]2-nonyl-2-propenoic acid, is a specific inhibitor for the redox function of hApe1. The interaction mechanism is not known. Using N-Ethylmaleimide (NEM) chemical footprinting, combined with Hydrogen/Deuterium Exchange (HDX) data, we propose that a locally unfolded form coexists with the folded form in an equilibrium that is driven by irreversible NEM labeling, and that E3330 interacts with and stabilizes this locally unfolded form. This locally unfolded form is thereby proposed to be the redox-active form. We further support this claim with LC-MS/MS analysis showing an increase of disulfide bonds induced by E3330 among the cysteines in the redox domain, which would be too far apart from each other in the folded form to form a disulfide bond. We also studied three analogs of E3330. The need for an E3330 analog is to develop a more efficient and effective compound that would allow for sub-micromolar levels of activity (E3330 requires a micromolar amount). Study of the analogs will also allow us to gain perspective of the mechanism or mechanisms of E3330’s activity in Ape1’s redox function.

Le carcinome hépatocellulaire est l'un des cancers les plus fréquents et des plus sévères à travers le monde. Le diagnostic est souvent tardif et les traitements curatifs ne peuvent être proposés qu'à un nombre limité de patients. Les technologies modernes ont permis le développement de nouvelles méthodes de radiothérapie qui montrent aujourd'hui de bons résultats. Par ailleurs, bien que des déficiences dans les voies de réparation de l'ADN soient associées à une instabilité génomique et une susceptibilité au cancer, une inhibition de ces voies sensibilise les cellules cancéreuses à la chimiothérapie et à la radiothérapie. Dans ce contexte, les inhibiteurs de poly(ADP-ribose) polymérases (PARP) ont déjà montré des résultats prometteurs dans des études pré-cliniques et sont en cours d'évaluation clinique pour de nombreux cancers. Ce travail de thèse a consisté en l'évaluation du potentiel des inhibiteurs de PARP en combinaison avec la radiothérapie comme nouvelle option thérapeutique pour le carcinome hépatocellulaire. La première étape de ce travail a été de caractériser les profils d'expression et d'activité de plusieurs membres de la famille PARP dans des cellules cancéreuses du foie et des hépatocytes primaires humains ainsi que dans des tissus hépatiques. En second lieu, nous avons étudié le potentiel de l'inhibiteur de PARP ABT-888 seul et en combinaison à des radiations ionisantes in vitro. Le traitement par l'inhibiteur de PARP ABT-888 en agent seul a montré une sensibilité variable des différentes lignées cellulaires étudiées à cette drogue. Afin de comprendre la sensibilité variable des cellules cancéreuses hépatiques à l'ABT-888, nous avons analysé leur capacité de réparation des dommages à l'ADN et avons observé des capacités différentes entre les lignées cellulaires. Finalement, nous avons pu montrer que l'ABT-888 sensibilise les cellules cancéreuses hépatiques aux radiations ionisantes. Ce travail de recherche a permis de montrer que les inhibiteurs de PARP ont un fort potentiel pour améliorer les méthodes de radiothérapie utilisées dans la prise en charge du carcinome hépatocellulaire / Hepatocellular carcinoma is the third cause of cancer related death. Due its often late diagnosis and advanced stage, a limited number of patients can benefit from curative treatments. There is thus a constant need for new treatment strategies for patients with hepatocellular carcinoma. Targeting DNA repair pathways to sensitize tumor cells to chemoor radiotherapeutic treatments is now a common strategy under investigation for cancer treatment with inhibitors of poly(ADP-ribose) polymerases (PARP) showing great potential. The aim of this work was to evaluate the potential of PARP inhibitors alone and in combination with radiation therapy as a new strategy for the treatment of hepatocellular carcinoma. We first analyzed the expression and activity of different PARP genes in a panel of liver cancer cell lines and primary human hepatocytes as well as their DNA repair capacity and assess the impact of PARP inhibitors alone and in combination with ionizing radiation in these models on cell survival. A large range in expression of PARP family members, PARP activity and sensitivity to ABT-888 in the panel of liver cells was observed as well as differential excision/synthesis repair capacity. Finally, we showed that ABT-888 sensitizes liver cancer cells to the cell killing effects of ionizing radiation. PARP inhibitors show great potential for improving radiation therapy strategies used in the management of hepatocellular carcinoma

Ce travail de thèse porte sur l’étude des ARN polymérases ARN dépendant impliquées dans le RNA silencing chez Arabidopsis thaliana. Durant ma thèse, la recherche d'interacteurs des RDR, parmi des protéines impliquées dans le RNA silencing, a permis la détection d'interaction entre RDR6 et SDE3, RDR6 et SGS3, mais aussi entre SDE3 et SGS3 en Co-IP et BiFC. Une co-localisation de ces protéines a été observée lorsqu'elles sont produites transitoirement dans des cellules épidermales de N. benthamiana.Un crible d’une banque d’ADNc d’A. thaliana par double hybride de levure, a permis d’isoler des interacteurs potentiels de RDR6. Deux interacteurs potentiels, AtUAP56-1 et U2B’’, sont impliqués dans l’épissage des précurseurs des ARNm. Un effet sur le RNA silencing dans des mutants de l’épissage en 3’ des ARNm était connu et nous avons confirmé l’interaction entre RDR6 et AtUAP56-1 par BiFC. L’étude de lignées mutantes pour AtUAP56-1 a donc été initiée.Une étude biochimique de RDR6 et de RDR2 a été réalisée. Des formes recombinantes de RDR2 et RDR6 ont été produites de façon transitoire dans des feuilles de N. benthamiana, et une étude comparative de RDR2 et RDR6 a été réalisée. Les deux RDR sont actives sur des matrices ARN et ADN, et montrent in vitro une activité amorce-indépendante. De plus, nous avons détecté pour la première fois une activité amorce-dépendante de RDR6 et RDR2. Ces résultats apportent de nouvelles données biochimiques qui sont en accord avec les études menées in vivo et enrichissent les modèles actuels du RNA silencing. / The aim of this work was to study RNA-dependent RNA polymerases involved in RNA silencing in Arabidopsis thaliana. During my thesis, the search for RDR interactors among proteins involved in RNA silencing allowed the detection of interactions between RDR6 and SDE3, RDR6 and SGS3, and also between SDE3 and SGS3 using Co-IP and BiFC. In addition, the co-localisation of these proteins was observed when produced transiently in epidermal cells of N. Benthamiana.A screen of an A. thaliana cDNA library by yeast two hybrid allowed us to identify some putative new RDR6 interactors. Two putative RDR6 interactors, AtUAP56 and U2B’’, are known to be involved in pre-miRNA splicing. Furthermore, a link between pre-mRNA 3’ splicing and RNA silencing was previously reported. We also confirmed the interaction between AtUAP56-1 and RDR6 by BiFC. An investigation of A. thaliana of AtUAP56-1 mutants has been initiated.Recombinant RDRs were produced transiently in N. Benthamiana, and a biochemical comparative study of RDR2 and RDR6 performed. We found that RDR2, like RDR6, has a de novo polymerase activity on DNA and RNA templates, and for both RDRs we also showed, for the first time, a primer-dependant synthesis of dsRNA from RNA template. These findings provide important new insights into our understanding of the molecular mechanisms of RNA silencing amplification in Arabidopsis.

A bactéria Escherichia coli é encontrada em diversos habitats e deve estar preparada para sobreviver e crescer em condições desfavoráveis. A adaptação da bactéria a diferentes condições obriga-a a controlar a expressão de genes de forma eficiente. Uma das formas primárias de controle de expressão gênica é a competição entre os diversos fatores sigma pela ligação ao cerne da RNA polimerase. <font face=\"Symbol\">d70 é o fator sigma mais abundante e participa da transcrição da maioria dos genes de E. coli, enquanto que <font face=\"Symbol\">dS é o segundo em importância e reconhece promotores de genes relacionados à resposta geral ao estresse. O gene rpoS, que codifica para <font face=\"Symbol\">dS é altamente polimórfico, e adquiri mutações frequentemente. A mutação pontual C<font face=\"Symbol\">&#174;T na posição 97 da ORF de rpoS, resulta em um códon de parada TAG (âmbar). Um Shine-Dalgarno alternativo e um códon de início de tradução na posição 157 dá início a uma proteína RpoS truncada, que é parcialmente funcional. Uma das situações de estresse na qual <font face=\"Symbol\">dS é ativado corresponde à privação de fosfato inorgânico. Porém, na limitação deste nutriente ocorre também a ativação do regulon PHO, cujos genes são predominantemente transcritos por <font face=\"Symbol\">d70. Neste trabalho, o efeito da versão truncada de RpoS sobre a expressão de genes dependentes de <font face=\"Symbol\">d70 (lacZ, phoA e pstS) e de genes dependentes de <font face=\"Symbol\">dS (osmY e proU) foi testado. Foram também realizados ensaios de estresse oxidativo, osmótico e pelo frio. O perfil de atividade parcial descrito para RpoSam pôde ser observado em alguns casos, porém em outros o comportamento deste alelo se assemelhou ao do mutante rpoS nulo. Paralelamente, foi testada também uma cepa de E. coli que carrega a mutação âmbar em rpoS, mas esta é suprimida, resultando na expressão de uma proteína RpoS normal. A proteína RpoS truncada não pôde ser visualizada em immunoblots, provavelmente porque esta é traduzida de forma pouco eficiente a partir do Shine-Dalgarno alternativo. Com o objetivo de incrementar a detecção de RpoS em ensaios de imuno-detecção, foi inserida por recombinação alélica uma etiqueta SPA altamente imunogênica na porção C-terminal da proteína. / Escherichia coli can be found in many different habitats and has to be prepared to survive and grow under unfavorable conditions. Bacteria adaptation to different growth conditions requires an efficient control of gene expression. One of the primary forms of gene expression control is the competition between different sigma factors for the binding to the core RNA polymerase. <font face=\"Symbol\">d70 is the most abundant sigma factor and participates in the transcription of most E. coli genes. <font face=\"Symbol\">dS is the second one in importance and recognizes promoters of genes related to the general stress response. The rpoS gene, which encodes <font face=\"Symbol\">dS, is highly polymorphic and acquires mutations very often. The transition C<font face=\"Symbol\">&#174;T at position 97 in the rpoS ORF results in a stop codon TAG (amber). Due to the presence of an alternative Shine-Dalgarno and a translation initiation codon at position 157 a truncated RpoS protein that is partially functional is translated. One of the stress situations that <font face=\"Symbol\">dS is activated is the starvation for inorganic phosphate. Phosphate limitation also triggers the activation of the PHO regulon, whose genes are predominantly transcribed by <font face=\"Symbol\">d70. In the present study, the effect of the truncated version of RpoS on the expression of <font face=\"Symbol\">d70 dependent genes (lacZ, phoA e pstS) and <font face=\"Symbol\">dS dependent genes (osmY e proU) was tested. Bacteria were also assayed for sensitivity to oxidative, osmotic and cold stress. The profile of partial activity described for the truncated RpoS could be observed in some cases, while in others the behavior of this allele resembled the rpoS null mutant. In parallel, an E. coli strain which suppresses the amber mutation in RpoS, resulting in the expression of a normal protein was also tested. A band correponding to the truncated RpoS could not be detected in immunoblots probably due to inefficient translation from the alternative Shine-Dalgarno. To improve the detection of RpoS, a highly immunogenic SPA tag was inserted in the C-terminal region of the protein.

Thesis (Ph.D.)--University of Alberta, 2010. / A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Virology, Medical Microbiology and Immunology. Title from pdf file main screen (viewed on January 10, 2010). Includes bibliographical references.