Yes / Cancer-causing mutations often arise from inappropriate DNA repair, yet acute exposure to DNA damage is widely used to treat cancer. The challenge remains in how to specifically induce excessive DNA damage in cancer cells while minimizing the undesirable effects of genomic instability in noncancerous cells. One approach is the acute exposure to hyperthermia, which suppresses DNA repair and synergizes with radiotherapy and chemotherapy. An exception, however, is the protective effect of hyperthermia on topoisomerase targeting therapeutics. The molecular explanation for this conundrum remains unclear. Here, we show that hyperthermia suppresses the level of topoisomerase mediated single- and double-strand breaks induced by exposure to topoisomerase poisons. We further uncover that, hyperthermia suppresses hallmarks of genomic instability induced by topoisomerase targeting therapeutics by inhibiting nuclease activities, thereby channeling repair to error-free pathways driven by tyrosyl-DNA phosphodiesterases. These findings provide an explanation for the protective effect of hyperthermia from topoisomerase-induced DNA damage and may help to explain the inverse relationship between cancer incidence and temperature. They also pave the way for the use of controlled heat as a therapeutic adjunct to topoisomerase targeting therapeutics.

Afin de transmettre leurs informations génétiques d'une génération à l'autre, les organismes à reproduction sexuée doivent réduire de moitié leur contenu chromosomique pour former des gamètes haploïdes. Cette réduction se produit lors d'une division cellulaire appelée méiose, durant laquelle une étape de réplication est suivie de deux divisions successives, la méiose I et II. Au cours de la méiose I, les chromosomes homologues se séparent et leur bonne ségrégation dépend de la création entre eux d’un lien physique. En méiose c’est le processus de réparation appelé recombinaison homologue, qui à la suite de l’induction dans le génome de centaine de cassures double brin par la protéine Spo11, permet d’établir ce lien. Spo11 est l'orthologue méiotique de la sous-unité catalytique de la topoisomérase VI, TopoVIA. Comme TopoVI est composée de deux sous-unités, TopoVIA et TopoVIB, l’existence d’un orthologue méiotique de TopoVIB était une question posée depuis l'identification de Spo11. Au cours de ma thèse, j'ai contribué à identifier une nouvelle famille de protéine, que l’on a nommé TopoVIB-like, orthologue à TopoVIB et nécessaire à la formation des cassures double-brin d'ADN méiotiques(Robert et al, 2016). Ces protéines ont des domaines similaires à ceux de TopoVIB, à savoir un GHKL (impliqué dans la liaison et l'hydrolyse de l'ATP), un domaine transducteur et un domaine CTD. Nous avons démontré que chez la souris, SPO11 forme un complexe avec TOPOVIBL. De plus, nous avons démontré que cette protéine est nécessaire à la formation des CDB. Ces résultats suggèrent que chez la souris, les CDB méiotiques sont catalysées par un complexe TopoVI-like. Chez S. cerevisiae, il n'y a pas d'orthologue clair de TopoVIB, mais nous avons trouvé que la protéine Rec102, connue pour être nécessaire à la formation des CDB méiotiques, présente une homologie partielle avec le domaine transducteur des TopoVIB-like. Rec102 forme un complexe avec Rec104, une protéine également requise pour la formation des CDB. Ainsi, nous avons émis l'hypothèse que le complexe Rec102 / Rec104 était l'orthologue méiotique de TopoVIB chez la levure, interagissant avec Spo11 pour former un complexe de type TopoVI-like. Malgré l'importance de Spo11, son mode d'action est mal connu. Cette absence de données biochimiques est due à l’insolubilité de la protéine. Le but de ma thèse était de caractériser le mode d'action et la régulation du complexe TopoVI-like dans la formation des CDB méiotiques. Tout d'abord, biochimiquement, en purifiant in vitro une forme soluble du complexe TopoVI-like de levure composé de Spo11 / Rec102 / Rec104 / Ski8 (un partenaire direct de Spo11) en co-exprimant ces protéines dans deux systèmes d'expression, E. coli et S. cerevisiae. En utilisant E. coli, j'ai réussi à purifier un complexe soluble formé par Spo11 / Rec102 / Rec104 / Ski8 et en utilisant S. cerevisiae, j'ai purifié deux complexes différents, l'un formé par les quatre protéines, et un formé uniquement par Spo11 et Rec102. Néanmoins, les tests d'activité sur différents substrats d'ADN n'ont révélé aucune activité de coupure de l’ADN. Le deuxième objectif de ma thèse était d'étudier comment, chez la souris, TOPOVIBL régule l'activité de SPO11 en interagissant avec d'autres protéines nécessaires à la formation des CDB. En double hybride, j'ai prouvé que, comme chez la levure, l'orthologue méiotique de TopoVIB chez la souris interagissait avec REC114, une autre protéine nécessaire à la formation des CDB. La cartographie de cette interaction à l'échelle de l’acide aminé a conduit à l'identification d'un résidu sur TOPOVIBL essentiel pour l'interaction entre TOPOVIBL et REC114. Afin d'étudier in vivo le rôle de l'interaction entre TOPOVIBL et REC114, une souris mutante pour le résidu identifié de TOPOVIBL a été générée à l'aide de CRISPER-Cas9 et son phénotype a été analysé. / To properly transmit their genetic information from one generation to another, sexually reproductive organisms need to halve their genome to form haploid gametes. This reduction occurs during a special cell division called meiosis, which proceeds through one round of DNA replication followed by two successive divisions called meiosis I and II. During meiosis I homologous chromosomes segregate, and their proper segregation depends on the homologous recombination pathway that establishes a physical link between the homologues. During meiosis, homologous recombination events are triggered by the formation of DNA double strand break (DSB) catalyzed by the evolutionarily conserved Spo11 protein. Spo11 is the meiotic ortholog of the catalytic subunit of the TopoVI topoisomerase, TopoVIA. As TopoVI is composed of two subunits, TopoVIA and TopoVIB, the requirement for meiotic DSB formation of a B subunit was under investigation since the identification of Spo11. During my PhD, I contributed to the identification of a new family of protein, the TopoVIB-like family, ortholog to the Topoisomerase VI B subunit (TopoVIB) and required for meiotic DNA double strand break formation (Robert et al, 2016). These proteins share domains in part similar to the canonical TopoVIB which are a GHKL domain (involved in ATP binding and hydrolysis), a transducer domain and a CTD domain. We demonstrated that in mice, SPO11 forms a complex with TOPOVIBL. Biochemical characterization of this complex showed a structure compatible with an A2B2 organization. Furthermore, we demonstrated that this protein is required for meiotic DSB formation. These results suggest the existence, in mice, of a TopoVI-like complex that catalyzes the formation of meiotic DSB. In S. cerevisiae, there is no clear TopoVIB-like ortholog, but we found that the Rec102 protein, which is known to be required for the formation of meiotic DSB, shows a partial homology with the transducer domain of the TopoVIB-like proteins. Rec102 forms a complex with Rec104, a protein also essential for DSB formation. Thus, we hypothesized that the Rec102/Rec104 complex is the yeast meiotic ortholog of TopoVIB, interacting with Spo11 to form a meiotic TopoVI-like complex. Despite the importance of Spo11 little is known about its mode of action. This absence of biochemical data is due to the lack of solubility of the protein. The aim of my PhD was to characterize the mode of action and regulation of the TopoVI-like complex for meiotic DSB formation. First, biochemically, by purifying in vitro a soluble form of the yeast TopoVI-like complex composed by Spo11/Rec102/Rec104/Ski8. To achieve this objective, I co-expressed these proteins in two different expression systems, E. coli and meiotic culture of S. cerevisiae. Using E. coli I managed to purify a soluble complex formed by Spo11/Rec102/Rec104/Ski8, and using meiotic culture of S. cerevisiae, I purified two different complexes, one formed, by the four proteins, and one formed only by Spo11 and Rec102. Nevertheless, in vitro activity essays on different DNA substrates did not reveal any DNA cleavage activity. The second goal of my PhD was to study how in mouse, the activity of TOPOVIBL / SPO11 may be regulated by other proteins known to be required for DSB formation. Using Y2H experiment I was able to prove that, as in yeast, mouse TOPOVIBL interacts with REC114, a protein required for DSB formation. The mapping of this interaction at the amino-acid scale, leads to the identification of one residue on TOPOVIBL essential for the interaction between TOPOVIBL and REC114. In order to investigate in vivo the role of the interaction between TOPOVIBL and REC114, a mutant mouse carrying a mutation in the identified residue of TOPOVIBL was generated using CRISPER-Cas9, and its phenotype analyzed.

Among women in the 45 to 64 age group, over half of the recorded deaths are from cancer, breast cancer being the most common. Just over 30% off all deaths in New Zealand women is caused by breast cancer. Treatment of cancer is difficult, not only due to the physiological and immunological similarities between a cancer cell and a normal cell, but also due to the high cardiotoxicity of many treatments, and also the problems related with the development of resistance. Approximately 40% of the cancer cells treated with the chemotherapy drug doxorubicin will become resistant to treatment. Drug efficacy is strongly associated with the proliferation status of a cell, as cancer cells divide rapidly, this can often be the defining factor between effective treatments or the development of resistance. Central to this proliferation status is an enzyme known as topoisomerase IIa. This essential enzyme is expressed in all cells and is required to relieve the torsional stress in DNA that is created during normal cellular processes. A number of commonly used anti-cancer drugs have been found to target topoisomerase IIa in cancer cells and significantly, during the development of drug resistance levels of topoisomerase IIa enzyme have been found to be reduced in some cell lines and tumours. There are a number of factors that can modulate the amount of topoisomerase IIa enzyme found in a cell, and one of the ways to understand this is to examine the regulation of the topoisomerase IIa gene, most importantly the proteins that interact with the promoter region to direct transcription. The human topoisomerase IIa promoter has been found to be regulated by a number of transcription factors that can bind to their cognate sequences. The introduction of mutations within specific sequences of the topoisomerase IIa promoter has enabled the identification of a key regulatory region within the promoter, a sequence of DNA that encompasses both the ICB1 and GC1 regulatory elements. Transcription factor NF-Y is found to bind to ICB1 element, whereas transcription factors Sp1 and Sp3 have been found to associate with the GC element. However this region of the promoter was also found to bind a fourth uncharacterised component. This research aims to further define the protein components that are found to bind to this important ICB1/GC1 regulatory region and distinguish the protein-protein and protein-DNA interactions that are important for the regulation of the human topoisomerase IIa promoter.

Made available in DSpace on 2015-05-14T12:59:25Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 799830 bytes, checksum: e9ce4907eb8193bacb26ea198ef6011e (MD5) Previous issue date: 2011-02-15 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The Topoisomerase II is involved in several vital cellular processes such as replication and transcription of DNA, in addition to the segregation of chromosomes. This enzyme catalyzes changes in DNA topology by temporary disruptions and subsequent rearrangement of the double helix and is essential for cell proliferation to occur. Many compounds that interfere with the catalytic activity of this enzyme are effective in chemotherapy of cancer. The development of new inhibitors from plant sources can be a valuable strategy, serving also as a tool for the production of semi-synthetic active agents that do not cause serious damage to the body and with a lower cost. Has already been reported that some lignoids derived from plants have inhibitory action on DNA Topoisomerase II. Plants of the Lauraceae family are sources of bioactive lignoids. Among different species, there are the Licaria aurea and Licaria chrysophylla. In this study, 12 lignoids derived from both species were evaluated for their inhibitory effect on human DNA Topoisomerase II, using etoposide as action control of substances. Two of these compounds showed inhibitory activity against the human enzyme Topoisomerase II. These compounds are the lignan (2S,3S)-Dihydro-dehydrodiconiferyl alcohol-3-(-D-glycopiranosyl)-hexaacetate and the neolignan 1,4-Bis-(3, 4,5-trimethoxyphenyl)-2,3-dimethylbutane. / A Topoisomerase II está envolvida em diversos processos celulares vitais, como a replicação e a transcrição do DNA, além da segregação dos cromossomos. Essa enzima catalisa mudanças na topologia do DNA através de rupturas temporárias e posterior rearranjo da dupla hélice, sendo fundamental para que ocorra a proliferação celular. Muitos compostos que interferem na atividade catalítica dessa enzima são eficientes no tratamento quimioterápico de câncer. O desenvolvimento de novos inibidores a partir de fontes vegetais pode ser uma estratégia valiosa, podendo servir também como um instrumento adequado para a produção de agentes ativos semi-sintéticos que não causem danos graves ao organismo e que apresentem um menor custo. Já se tem reportado que alguns lignóides derivados de plantas têm ação inibitória sobre a DNA Topoisomerase II. Plantas da família Lauraceae são fontes de lignóides bioativos. Dentre as diversas espécies, encontra-se a Licaria aurea e a Licaria chrysophylla. No presente estudo, 12 lignóides derivados destas duas espécies foram avaliados quanto à sua capacidade inibitória sobre a DNA Topoisomerase II humana, utilizando a etoposida como controle de ação das substâncias. Dois dos compostos estudados apresentaram atividade inibitória sobre a enzima Topoisomerase II humana. Esses compostos são a lignana (2S,3S)-Dihidro-dehidrodiconiferil alcool-3-(-D-glicopiranosil)-hexaacetate e a neolignana1,4-Bis-(3, 4,5-trimetoxifenil)-2,3-dimetilbutano.

Human response to ionising radiation (IR) shows a wide variation. This is most clearly seen in the radiation-response of cells as measured by frequencies of chromosomal aberrations. Different frequencies of IR-induced aberrations can be conveniently observed in phytohaemagglutin-stimulated peripheral blood T-lymphocytes from both normal individuals and sporadic cancer cases, in either metaphase chromosomes or as micronuclei in the following cell cycle. Metaphase cells show frequent chromatid breaks, defined as chromatid discontinuities or terminal deletions, if irradiated in the G 2 -phase of the cell cycle. It has been shown that the frequency of chromatid breaks in cells from approximately 40% of sporadic breast cancer patients, are significantly higher than in groups of normal individuals. This suggests that elevated radiation-induced chromatid break frequency may be linked with susceptibility to breast cancer. It is known that chromatid breaks are initiated by a double strand break (DSB), but it appears that the two are linked only indirectly as repair kinetics for DSBs and chromatid breaks do not match. Therefore, the underlying causes of the wide variation in frequencies of chromatid breaks in irradiated T-lymphocytes from different normal individuals and from sporadic breast cancer cases are still unclear but it is unlikely to be linked directly to DSB rejoining. My research has focused on the mechanism through which chromatid breaks are formed from initial DSBs. The lack of a direct association suggested that a signalling process might be involved, connecting the initial DSB and resulting chromatid break. The signal model, suggested that the initial DSB is located within a chromatin loop that leads to an intra- or interchromatid rearrangement resulting in incomplete mis-joining of chromatin ends during the decatenation of chromatids during G 2 . It was therefore proposed that topoisomerase II alpha (topo IIα) might be involved, mainly because of its ability to incise DNA and its role in sister chromatid decatenation. During my PhD research I have used a strategy of altering topo II activity or expression and studying whether this alters IR-induced chromatid break frequency. The first approach involved cell lines that varied in topo IIα expression. The frequency of IR-induced chromatid breaks was found to correlate positively with topo IIα expression level, as measured in three different cell lines by immunoblotting, i.e. two cell lines with lower topo IIα expression exhibited lower chromatid break frequency. Topo II activity in these three cell lines was also estimated indirectly by the ability of a topo IIα poison to activate the G 2 /M checkpoint, and this related well with topo IIα expression. A second approach involved ‘knocking down’ topo IIα protein expression by silencing RNA (siRNA). Lowered topo IIα expression was confirmed by immunoblotting and polymerase chain reaction. SiRNA-lowered topo IIα expression correlated with a decreased IR-induced chromatid break frequency. In a third series of experiments cells were treated with ICRF-193, a topo IIα catalytic inhibitor. It was shown that inhibition of topo IIα also significantly reduced IR-induced chromatid breaks. I also showed that lowered chromatid break frequency was not due to cells with high chromatid break frequencies being blocked in G 2 as the mitotic index was not altered significantly in cells with lowered topo IIα expression or activity. These experiments show that topo IIα is involved in IR-induced chromatid break formation. The final experiments reported here attempted to show how topo II might be recruited in the process of forming IR-induced chromatid breaks. Hydrogen peroxide was used as a source of reactive oxygen species (reported to poison topo IIα) and it was shown that topo IIα under these conditions is involved in the entanglement of metaphase chromosomes and formation of chromatin ‘dots’ as well as chromatid breaks. Experiments using atomic force microscopy attempted to confirm these dots as excised chromatin loops. The possible role of topo IIα in both radiation- and hydrogen peroxide-induced primary DNA damage was also tested. It was shown that topo IIα does not affect radiation-induced DSBs, even though it does affect chromatid break frequency. Also, topo IIα does not affect hydrogen peroxide-induced DNA damage at low doses. The results support the idea that topo IIα is involved in the conversion of DSBs to chromatid breaks after both irradiation and treatment with hydrogen peroxide at a low concentrations. I have demonstrated that topo IIα is involved in forming IR-induced chromatid breaks, most likely by converting the initial DSBs into chromosomal aberrations as suggested by the signal model.

The thesis entitled “Design and Synthesis of Benzimidazole Based Templates in Duplex and Quadruplex DNA Recognition and in Topoisomerase Inhibition” deals with the design and synthesis of several benzimidazole based molecules and their interaction with duplex and quadruplex DNA structures. It also elucidates the inhibition effect of the compounds on the activity of topoisomerase I enzyme of parasitic pathogen Leishmania donovani. The work has been divided into five chapters. Chapter 1: An Introduction to DNA and its Interaction with Small molecules. The first chapter provides an introduction to the double helical structure of DNA and the central dogma that suggests the flow of genetic information from DNA to RNA to protein. This chapter also presents an overview on the various types of small molecules that interact with duplex and quadruplex structures of DNA or interfere with the activity of DNA targeted enzymes like topoisomerase. This chapter describes the importance of such molecules as chemotherapeutic agents. Chapter 2 deals with three isomeric, symmetrical bisbenzimidazole derivatives bearing pyridine on the two termini. The syntheses, duplex DNA binding and computational structure analyses of the molecules have been divided into two sections. Chapter 2A: Novel Symmetrical Pyridine Derivatized Bisbenzimidazoles: Synthesis and Unique Metal Ion Mediated Tunable DNA Minor Groove Binding. The first chapter deals with the synthesis and double stranded (ds) DNA binding characteristics of the three bisbenzimidazole derivatives. Despite being positional isomers, their relative binding affinities towards ds-DNA varied considerably. Fluorescence, circular dichroism and temperature dependent UV-absorption spectroscopy have been employed to characterize ligand-DNA binding interaction. All spectroscopic studies revealed the strong A-T selective DNA binding affinities of the p- and m-pyridine derivatized molecules (p-pyben and m-pyben respectively) and indicated dramatically weak binding interaction of the ortho derivative (o-pyben) to ds-DNA. Additionally, unique transition metal ion mediated tunable DNA binding shown by o-pyben has been described in this chapter. While the ds-DNA binding characteristics of p- and m-pyben remained unaffected in presence of metal ions, that of o-pyben could be reversibly ‘switched off’ in the presence of divalent transition metal ions like Co2+, Ni2+, and Cu2+. Addition of EDTA reversed the effects and DNA binding was again observed. This interesting observation provides valuable insight into the DNA recognition property of these isomeric bisbenzimidazole derivatives. Figure 1. Molecular structures of pyridine derivatized symmetrical bisbenzimidazoles. Chapter 2B: Differential Binding of Positional Isomers of Symmetric Bisbenzimidazoles on DNA Minor-Groove: A Computational study. To explain the weak DNA binding affinity of o-pyben, compared to p- or m-pyben, detailed ab initio/DFT computational analyses of the inherent structural features of the three isomers were performed both in the gas-phase and in water. The study revealed the presence of intramolecular hydrogen bond existing in the opyben, between the benzimidazole proton (H3) and the pyridine nitrogen (N1). Additionally, potential energy scans for rotation about the bonds connecting the pyridine-benzimidazole and benzimidazole-benzimidazole fragments were performed. This revealed surprising conformational rigidity existing in the o- isomer that resisted any out-of-plane twisting of the pyridine-benzimidazole fragment. The presence of intramolecular H-bonding was further confirmed by experimental determination of pKa of the three isomers. The molecules being bisbenzimidazole derivatives bound to the minor groove of ds-DNA, the benzimidazole protons forming hydrogen bonded interactions with the DNA bases. However in the o- derivative, the intramolecular hydrogen bonding made the crucial benzimidazole protons unavailable for DNA binding thereby leading to its poor interaction with DNA. Chapter 3. Novel Series of Anthra[1,2-d]imidazole-6,11-dione Derivatives: Synthesis, DNA Binding and Inhibition of Topoisomerase I of Leishmania donovani This chapter describes the synthesis of nine imidazole fused anthraquinone derivatives and their interaction with double-stranded DNA, investigated by UV-visible absorption spectroscopy and viscometric titrations. Figure 2. Molecular structures of the imidazole fused anthraquinone derivatives. All the molecules showed intercalative mode of binding to double stranded DNA, though their relative binding affinities were different. Next their inhibitory effects on the catalytic activity of topoisomerase I enzyme of Leismania donovani were investigated. L. donovani is the causative agent for human visceral leishmaniasis; a fatal disease affecting liver and spleen. Five out of the nine derivatives tested, proved to be extremely efficient inhibitors of the enzyme. Of them, three showed greater inhibition potency than camptothecin, a well-established topoisomerase I inhibitor and the precursor for several clinically useful anti-tumor drugs. The molecules were shown to inhibit by the stabilization of enzyme-DNA cleavable complex, and the inhibition efficiency was found to be highly dependent on the pKa of the side-chain nitrogen. These results provide useful insights towards developing more potent inhibitors of the parasitic enzyme. As the compounds are synthetically facile, chemically stable and possess long shelf life, they should be attractive candidates for design of novel family of topoisomerase I inhibitor. Indeed the nature of amine based side chain and its pKa would hold the key in such design. Chapter 4 deals with a series of symmetrical bisbenzimidazole derivatives in which the benzimidazole units have been connected via different aromatic linkers. The syntheses, duplex DNA interaction, topoisomerase inhibition and quadruplex DNA stabilization shown by these four molecules have been divided into two sections. Chapter 4A. Synthesis, Duplex DNA Binding and Topoisomerase I Inhibition by Symmetrical Bisbenzimidazole Derivatives with Aromatic Linkers. This chapter describes the synthesis of four symmetrical bisbenzimidazole derivatives bearing aromatic linkers, phenyl, naphthyl or anthryl between the benzimidazole rings. Next their interaction with duplex DNA was investigated using fluorescence and temperature dependent UV absorption spectroscopy and viscometric titration techniques. Addition of DNA caused fluorescence enhancement of the molecules implying their interaction with duplex DNA. All the four molecules on binding to double helical DNA induced thermal stabilization of the latter. Viscometric titration of calf thymus DNA with the four compounds revealed a partial-intercalative mode of binding for the anthracene derivatized molecule 4. Next, their inhibitory effects on the catalytic activity of topoisomerase I enzyme were studied. The anthracene derivatized compound (4) showed high inhibition of the enzyme catalyzed relaxation of supercoiled plasmid DNA. Naphthalene derivatized compound (3) exhibited weak inhibition whereas the derivatives bearing 1,4- and 1,3-disubstitued benzene (1 and 2 respectively) units showed no inhibition. Figure 3. Molecular structures of the symmetrical bisbenzimidazole derivatives. Chapter 4B. Quadruplex DNA Stabilization by Symmetrical Bisbenzimidazole Derivatives with Aromatic Linkers. The ability of the aforementioned molecules to stabilize G-quadruplex structures was investigated next. DNA quadruplex secondary structures are potential molecular targets for new generation chemotherapeutic drugs; hence there is an impetus in developing quadruplex targeting molecules. The Tetrahymena thermophilia telomeric sequence 5´-(T2G4)4-3´ was selected for the studies as it exhibits interesting structural polymorphism depending on whether quadruplex formation occurs in presence of Na+ or K+. Circular dichroism and fluorescence anisotropy techniques were used to study the interaction of these newly synthesized molecules with quadruplex DNA. Also thermal stabilization of quadruplex structure induced by the molecules was determined by temperature dependent UV absorption studies. The compounds 1, 3 and 4 stabilized Na+ induced quadruplex without causing any structural alterations of the latter. However, the m-phenyl linker bearing molecule 2, above a certain [ligand]/[DNA] concentration ratio, caused uniquestructural alteration of the Na+ induced quadruplex such that the CD-signature of the latter resembled that of a K+ induced quadruplex structure. This result was corroborated by quadruplex thermal melting data and fluorescence anisotropy. Interestingly this ligand was also able to induce secondary structure formation in randomly oriented ss-DNA, akin to K+ induced quadruplex structure, even in the absence of Na+ or K+. Chapter 5. Synthesis and DNA Binding of Novel Biscationic Dimers of Bisbenzimidazole Systems. This chapter describes the design, synthesis and ds-DNA binding properties of four dicationic dimers of bisbenzimidazoles. Targeting long base pair sequences in double helical DNA is a key issue in chemical biology and connecting different DNA binding modules by appropriate linkers is an attractive strategy for achieving the same. The precursor monomer unit was a bisbenzimidazole derivative and an analogue of Hoechst 33258. Two such moieties were connected via bisoxyethylenic or 6- or 3-methylenic or piperazinyl units to achieve linker of varying length, rigidity and hydrophilicity. To study the interaction of the dimers with duplex DNA, fluorescence and circular dichroism spectroscopy were used. Two of the dimers, (bbim-2ox-bbim and bbim-6met-bbim) bearing long flexible spacers, were able to target 13-AT base pairs long oligonucleotide sequences in a 1:1 binding mode with an affinity 8-10 times better than the precursor monomer or Hoechst 33258. Also thermal denaturation experiments showed high duplex stabilization induced by the same two dimers. All studies indicated a bidentate mode of binding where both the arms of the dimers participated in DNA binding. The molecules bearing the short and rigid linkers (bbim-3met-bbim and bbimpiper- bbim) on the other hand showed low binding affinity towards duplex DNA, as indicated by fluorescence, circular dichroism and thermal melting studies. The short linkers probably did not favor simultaneous binding of both the monomeric arms of the dimers to DNA minor groove. The work reported in this chapter indicates the strong influence of the length and nature of linker in determining drug/DNA binding affinity. Figure 4. Molecular structures of dicationic dimeric bisbenzimidazole derivatives.(Refer PDF File)

Streptococcus pyogenes ist ein humanpathogenes Bakterium, welches verschiedene Gewebe besiedeln kann und dadurch unterschiedliche Krankheiten verursacht. Die enorme Anpassungsfähigkeit des Bakteriums beruht auf dessen Fähigkeit, verschiedene, vom Wirt induzierte Stresskonditionen zu ertragen. Genetische Faktoren, die in diesem Zusammenhang eine Rolle spielen, sind Toxin-Antitoxin (TA) Systeme. Typ II TA Systeme kodieren für zwei Proteine, ein Toxin und ein Antitoxin, die einen stabilen TA Komplex bilden. Verschlechtern sich die Wachstumsbedingungen, kann das Antitoxin proteolytisch abgebaut werden, wodurch das freigesetzte Toxin essentielle zelluläre Prozesse des Bakteriums inhibiert. In dieser Studie charakterisierte ich zwei chromosomal kodierte ParDE TA Systeme des pathogenen Bakteriums S. pyogenes. Ähnlich zu anderen Systemen werden das Toxin und das Antitoxin beider hier charakterisierten Systeme co-transkribiert und durch Stresseinwirkung (z.B. Aminosäure-mangel) induziert. Zudem konnten weitere posttranskriptionelle bzw. posttranslationale Mechanismen zur Regulierung der Genexpression beider Systeme nachgewiesen werden. Die extrachromosomale Expression der Toxine ParE1 und ParE2 führten in S. pyogenes und Escherichia coli zum Zelltod, wobei die Co-expression der entsprechenden Antitoxine ParD1 und ParD2 die Toxizität minderte. Allerdings verursachte die Überexpression der Antitoxine allein ebenfalls eine Inhibierung des Zellwachstums. ParD1 hemmte die Zellteilung in E. coli, wobei der N-Terminus des Proteins entscheidend für diesen Effekt zu sein schien. Zusammengefasst erweitern die Ergebnisse dieser Arbeit unser Verständnis von ParE Toxinen und verdeutlichen die diversen Mechanismen, welcher sich TA Systeme bedienen, um die bakterielle Physiologie zu beeinflussen. Zusätzlich gibt diese Arbeit einen Einblick in mögliche Mechanismen, die S. pyogenes implementiert, um Stresskonditionen im Wirt zu überdauern. / Streptococcus pyogenes is a human pathogen with a remarkable ability to colonize different tissues and to endure diverse host-induced stress conditions through mechanisms that have yet to be fully understood. One strategy employed by bacteria to cope with changing environments are toxin-antitoxin (TA) genetic modules. Under non-ideal conditions, the antitoxin is subject to proteolysis and thus the freed toxin protein can target crucial pathways in the cell modulating bacterial growth. This study, describes the characterization of two chromosomally encoded ParDE-like TA systems from the human pathogen S. pyogenes. The antitoxin-toxin genes of the parDEF1 and parDE2 TA systems are co-transcribed and triggered by stress-induced conditions. The parDE2 TA showed an inspected mRNA processing under amino acid starvation which suggest a putative post-transcriptional regulation. At the post-translational level, both systems are controlled by ClpXP antitoxin-protein degradation in vivo, an important factor for TA triggering. Furthermore, bacterial plasmid-based expression of the toxins ParE1 and ParE2 resulted in effects in cell viability while the antitoxin molecules ParD1 and ParD2 were able to prevent the toxins lethality, respectably. Unlike canonical antitoxins, both ParD1 and ParD2 molecules also displayed deleterious effects, which seemed to be exclusive and related with the N-terminus domain potentially involved in DNA-interaction. Finally, the ParE toxins presented remarkable plasticity, able to harm not only gyrase but also topoisomerase IV, two important bacterial drug targets that modulate DNA-topology. These results expand the view on the ParE molecular targets and highlight the diverse mechanisms TAs employ to modulate bacterial physiology. We also provide more insights into possible mechanisms that S. pyogenes employs to endure stress in the host and efficiently cause disease.

<p>Eukaryotic Topoisomerase 2 is an essential enzyme that solves DNA topological problems such as DNA knotting, catenation, and supercoiling. It alters the DNA topology by introducing transient double strand break in one DNA duplex as a gate for the passage of another DNA duplex. Two different aspects of studies about eukaryotic Topoisomerase 2 will be covered in this thesis. In the first half of the thesis, we investigated conformational changes of human Topoisomerase 2&#61537; (hsTop2&#61537;) in the presence of cofactors and inhibitors. In the second half, we focused on an unknown regulatory function in the C-terminal domain (CTD) of Drosophila Topoisomerase 2 (Top2).</p><p>In the project of studying enzyme conformational changes, we adapted a previously developed methodology, Pulse-Alkylation Mass Spectrometry, with monobromobimane to study the protein dynamics of hsTop2&#61537;. Using this method, we captured the evidence of conformational changes in the presence of ATP and Mg2+ or the Top2 inhibitor, ICRF-193 which were not previously observed. Last, by using CTD truncated hsTop2&#61537;, the increasing reactivity of Cys427 suggested the CTD domain might be tethered adjacent to the core enzyme.</p><p>Following the study of enzyme conformational changes, we switched gear to examine an interaction between Drosophila Top2 and Mus101, homolog of human TopBP1. We first found that Mus101 interacts with CTD of Top2 in a phosphorylation-dependent manner. Next, in the co-immunoprecipitation and pull-down experiments using truncated or mutant Top2 with various Ser to Ala substitutions, we mapped the binding motif to the last amino acids of Top2 and identified that phosphorylation of Ser1428 and Ser1443 is important for Top2 to interact with the N-terminus of Mus101, which contains BRCT1/2 domains (BRCT, BRCA1 C-terminus). The binding affinity of the N-terminal Mus101 with a synthetic phosphorylated peptide covering the last 25 amino acids of Top2 (with pS1428 and pS1443) was determined by surface plasmon resonance with a Kd of 0.57 &#956;M. In an in vitro decatenation assay, Mus101 can specifically reduce the decatenation activity of Top2, and dephosphorylation of Top2 attenuates this response to Mus101. Next, we endeavored to establish a cellular system for testing the biological function of Top2-Mus101 interaction. Top2-silenced S2 cells rescued by Top2&#61508;20, truncation of 20 amino acids from the C-terminus of Top2, developed abnormally high chromosome numbers, which implies an infidelity in chromosome segregation during mitosis. Lastly, Top2-null flies rescued by Top2 with S1428A and S1443A were found to be viable but sterile. After investigating spermatogenesis, telophase of meiosis I was delayed, indicating Top2-Mus101 interaction is also important in segregating DNA in meiosis.</p> / Dissertation

Ganoderma lucidum is a popular herbal medicine used in China to promote health. Modern studies have disclosed that the active ingredients of Ganoderma can exhibit several effects, including antitumor effects and immunomodulation. The present study evaluated the antitumor effects of self-prepared Ganoderma extracts and spores oil, and investigated the possible underlying mechanisms by observing the effects of the extracts and oil on topoisomerases and the cell cycle. The results showed that Ganoderma extracts and spores oil presented dose-dependent inhibitory effects on tumor cells. The half maximal inhibitory concentration (IC50) values of Ganoderma extracts on HL60, K562 and SGC-7901 cells for 24 h were 0.44, 0.39 and 0.90 mg/ml, respectively; for Ganoderma spores oil, the IC50 values were 1.13, 2.27 and 6.29 mg/ml, respectively. In the in vivo study, the inhibitory rates of Ganoderma extracts (4 g/kg/d, intragastrically) on S180 and H22 cells were 39.1 and 44.6%, respectively, and for Ganoderma spores oil (1.2 g/kg/d, intragastrically) the inhibitory rates were 30.9 and 44.9%, respectively. Ganoderma extracts and spores oil inhibited the activities of topoisomerase I and II. Ganoderma spores oil was shown block the cell cycle at the transition between the G1 and S phases and induce a marked decrease in cyclin D1 levels in K562 cells, with no significant change in cyclin E level. These results suggest that the Ganoderma extracts and spores oil possessed antitumor effects in the in vitro and in vivo studies. The antitumor mechanisms of the extracts and spores oil were associated with inhibitory effects on topoisomerase I and II activities, and for Ganoderma spores oil, the antitumor effects may also be associated with decreased cyclin D1 levels, thus inducing G1 arrest in the cell cycle.

Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Biochemical Sciences Candidate: Aneta Karešová Supervisor: PharmDr. Anna Jirkovská, PhD. Title of diploma thesis: DNA-protein covalent complexes detection as the means for the assessment of the DNA damage induced by topoisomerase poisons. Topoisomerase II is essential cellular enzyme, which modifies the secondary structure of DNA. By introducing a temporary double strand break to DNA it relieves a structural tension raised during transcription and translation. Absolutely indispensable is the role of topoisomerase II in the separation of sister chromatids synthesized in the S-phase of the cell cycle. The mechanism of DNA cleavage involves a covalent bond formed between active site tyrosine and 5' phosphate on both of the DNA strands and through the formed break the other strand or the other DNA molecule can pass. After that, the DNA strands are rejoined and topoisomerase II is detached. The indispensability of topoisomerase II mainly for proliferating cells makes it a great target for the antineoplastic drugs and the molecules belonging to the class of topoisomerase II inhibitors (etoposide, anthracyclines) are amongst the most useful anticancer drugs in the clinical practice. These clinically used "topoisomerase...