A G-quadruplex (GQ) is a type of noncanonical nucleic acid structure that can form in regions of nucleic acids rich in guanine nucleotides. The guanine bases form a square planar conformation via Hoogsteen hydrogen bonding. These stacked tetrads have inward-facing carbonyl oxygens, facilitating the coordination of ions. Improper GQ conformations can lead to improper regulation of gene expression, potentially resulting in genetic diseases or cancer. Here, we performed molecular dynamics simulations using the Drude polarizable force field (FF) to gain insight into factors contributing to the stability of two GQs. One is the bcl-2 promoter region GQ, which is implicated in several types of cancer including B-cell lymphoma, and the second is the sc1 RNA GQ, which binds to the Fragile-X Mental Retardation Protein (FMRP) and is implicated in the development of Fragile X Syndrome (FXS). Aberrant bcl-2 GQ conformations result in increased production of the BCL2 protein, which is an apoptosis inhibitor. As such, we aim to characterize the factors stabilizing the GQ for future small-molecule development to prevent apoptosis inhibition and therefore cancer. The FMRP protein functions as a regulator of sc1 conformation to control the translation of proteins required for frontal lobe development. FXS arises from a nonsense mutation that causes the deletion of the C-terminal region of FMRP, rendering it non-function. Therefore, we aim to simulate sc1 when FMRP is bound as well as unbound to provide insight into the types of interactions that must be maintained and therefore mimicked by a small molecule drug. / Master of Science in Life Sciences / DNA is commonly represented as a double helix and RNA is thought of as a simple single stranded, disordered molecule, but DNA and RNA can both adopt more complicated structures. An example of this is the G-quadruplex (GQ), a structure that can form in regions of DNA and RNA that are rich in guanine. These guanine bases form a stable core structure that can act as an "on-off" switch for different processes in the cell. Alterations to GQ structure can lead to dysfunction and different types of disease. Here, we perform atomistic computer simulations to further understand factors that contribute to GQ stability, focusing on two different GQs, one of plays a role in several types of cancer, and the other whose regulation is in Fragile X Syndrome (FXS). Furthermore, we study the Fragile X Mental Retardation Protein, which is what brain cells normally use to regulate expression of proteins needed for frontal lobe development by modulating specific GQ structure. The information from these simulations can be used to potentially develop drugs for these conditions.

Les structures G-quadruplexes (G4) sont considérées comme des obstacles qui s’opposent à la progression du réplisome. Les séquences capables de former des G4 dans le génome humain se trouvent dans les régions d’ADN double brin au niveau des oncogènes et des proto-oncongènes et sur l’extrémité simple brin des télomères. La plupart des études biochimiques et biophysiques ont caractérisé les propriétés thermodynamiques des G4 en utilisant par exemple la température de fusion Tm pour déduire la thermodynamique de la formation/résolution du G4. Cependant, les expériences en solution donnent seulement une information indirecte concernant la dynamique du G4. Dans ce travail de thèse en molécule unique utilisant la technique des pinces magnétiques, nous avons pu caractériser la cinétique de la formation et résolution des G4s ainsi que la stabilité d’une structure G4 insérée dans une région d’ADN double brin : une situation qui ressemble aux G4 dans les promoteurs de gènes, où la séquence complémentaire est en compétition avec la formation de la structure de G4. Nous avons trouvé que le G4 télomérique a une très courte durée de vie (~20 s) et donc ce G4 se résout sans qu’une hélicase soit nécessaire. Au contraire, ce n’est pas le cas pour le G4 du c-MYC qui est très stable (~2h). Nous avons observé en temps réel la collision entre les hélicases et les polymérases et le G4 du c-MYC. Nous avons trouvé que l’hélicase Pif1 ouvre l’ADN puis résout le G4 après avoir effectué une pause et reprend l’ouverture de l’ADN, alors que l’hélicase RecQ et l’hélicase réplicative du bactériophage T4 ne peuvent pas le résoudre, mais peuvent le sauter. Nous avons aussi trouvé que la RPA ne peut pas résoudre le G4 du c-MYC. D’autre part, nous avons observé que la polyémrase du virus T4, la gp43, ainsi que la polymérase de T7, et la polymérase ε de la levure peuvent répliquer le G4 du c-MYC qui de façon étonnante ne constitue pas une barrière infranchissable. / G-quadruplex (G4) structures are considered as the major impediments for the replisome progression. The putative G4 forming sequences in the human genome are mostly located in the double-stranded DNA regions of oncogenes and proto-oncogenes and on the single-stranded overhangs of telomeres. Most of the biochemical and biophysical studies have characterized the G4 thermodynamics properties using melting temperature Tm as a proxy to infer thermodynamics of G4 folding/unfolding energetic. However, these thermodynamics properties give only indirect information about G4 dynamics. In this work, using single molecule magnetic tweezers technique, we first characterize the kinetics of folding and unfolding and thus the stability of a single G4 inserted in a dsDNA: a situation that mimics the G4s in promoters, where the complementary sequence competes with the G-rich structure. We find that the lifetime of telomeric G4 is short (~20 s) and thus that this G4 unfolds without the need of a helicase. This is not the case for the very stable c-MYC G4 (~2 hr). We observe in real time how helicases or polymerases behave as they collide with the c-MYC G4 on their track. We find that the Pif1 helicase unwinds dsDNA, resolves this G4 after pausing and resume unwinding, while RecQ helicase and the bacteriophage T4 replicative helicase do not resolve the G4 but may jump it. We also find that RPA does not unfold the c-MYC G4. Besides, we find that T4 bacteriophage gp43 polymerase, T7 polymerase and Yeast Pol ε can replicate the G4 which surprisingly does not appear as a major roadblock for them.

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Les oligopyridine-dicarboxamides et les oligoquinoline-carboxamides sont des oligomères synthétiques capables d’adopter des conformations hélicoïdales stables et bien définies. Les premiers sont comparables à des ressorts moléculaires qui peuvent s’étirer puis s’autoassembler pour former des doubles hélices artificielles. L’étude structurale d’oligopyridines de différentes tailles par diffraction des rayons X et RMN a permis d’éclaircir les principes de l’hybridation en double hélice. Par exemple, nous constatons que la stabilité du duplex est d’autant plus grande que l’oligomère est long mais la cinétique de l’hybridation décroit avec la taille des hélices. Ces propriétés sont modulables en fonction de divers paramètres tels que le solvant ou les substituants des pyridines. Les seconds forment de simples hélices moléculaires stables dans les solvants organiques mais aussi dans l’eau. Nous avons développé leur synthèse sur support solide afin de disposer de séquences variées, à l’image des alpha-peptides. Des études par RMN suggèrent que l’introduction d’unités aminométhylpyridines au sein d’un oligoquinoline hydrosoluble apporte de la flexibilité sans perturber sa structure hélicoïdale. Cela témoigne de la stabilité de ces structures secondaires dans les solvants protiques. Par ailleurs, certains de ces peptidomimes s’avèrent capables de reconnaitre et stabiliser des motifs structuraux particuliers de l’ADN : les G-quadruplex. Etant donné que ces architectures se forment à des endroits clés du génome impliqués dans des cancers, ces hélices moléculaires font figure de potentiels agents antitumoraux d’un nouveau genre. / Oligopyridine-dicarboxamides and oligoquinoline-carboxamides are synthetic oligomers able to fold into stable and well defined helical conformations. The first ones are comparable to molecular springs which can extend then associate to form artificial double helices. A structural study of oligopyridines of various sizes by X-ray diffraction and NMR provided a better understanding of the hybridization process. For example, we noticed that the stability of the duplex is all the higher as the oligomer is long but the kinetics of hybridization decrease with length. These properties depend on diverse parameters such as the solvent or the substituants of pyridine rings. The second family forms stable single helices in organic solvents and also in water. We adapted their synthesis on solid support to promote accessibility to a variety of sequences, just like for alphas-peptides. NMR studies suggested that the introduction of aminomethylpyridine units within a hydrophilic oligoquinoline strand brings some flexibility without disrupting its helical structure, showing the high stability of these secondary structures in protic solvents. Besides, some of these peptidomimetics turn out to be capable of recognizing and stabilizing a particular DNA motif: G-quadruplex structure. Given that these architectures form in critical places of the genome involved in cancers, these molecular helices may represent a new class of potential antitumoral agents.

Targeting oncogene promoters: a novel heterocyclic cations as G-quadruplex stabilizing ligands Lenka Pohlová Abstract: The diploma thesis studies an effect of newly synthesized group of compounds - helquats - on the expression of c-myc as a major player in malignant transformation and tumorigenesis via the stabilization of G-quadruplex in c-myc promotor. The G-quadruplex c-myc stabilization ability was tested for 101 helquats using dual luciferase reporter assay. The G-quadruplex c-myc stabilization ability was found for 13 helquats by this method. 8 successful helquats was selected by a comparison of the results from dual luciferase reporter assay and FRET melting assay. Effect on cell viability of tumor (HeLa S3) and non-tumor (HUVEC) cell lines was evaluated for these 8 helquats. Three of them exhibited cytotoxic effect on tumor cells but no effect was observed on viability of non-tumor cells. Moreover, an effect of these 3 helquats on c-myc expression on both mRNA and protein level, where significant effect on c-myc mRNA expression was not found for most of incubation periods. The 30% decrease in mRNA level was observed only for 24 hours incubation period for two helquats (LS702 and MJ656). The decrease in the expression on protein level was observed for all tested helquats, and helquat LS702 had the...

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Telomeres are nucleoprotein complexes found at the ends of linear eukaryotic chromosomes. Telomeres consist of a short sequence of repetitive double stranded DNA, TTAGGG repeats in humans (and all mammals), and a complex of 6 proteins, termed the shelterin complex. The length of the telomeres varies greatly between species, from approximately 300 base pairs in yeast to many 10-15 kilo bases in humans, because of the end replication problem this length get shorten with each cell division and ultimately leads to cell death. However the immortal eukaryotic cells and some transformed human cells over come this incomplete end replication problem with the use of enzyme called Telomerase. Telomerase is a ribonucleoprotein enzyme that adds a specific DNA sequence repeats (TTAGGG) to the 3¢ end of DNA strands in the telomere regions. However from the telomerase activity studies, it was concluded that telomerase is active in almost 90% of human cancers but not in normal somatic tissues. Finally, the low or transient expression of telomerase in normal tissues, including normal stem cells, and the generally longer telomeres in normal cells versus tumor cells provide a degree of tumor specificity to telomerase-based drugs and reduce the probability of toxicity to normal tissue. All of these factors suggest that cancer drugs based on telomerase might have a broad therapeutic window. This dissertation focusing on the synthesis of acridine derivatives that have the capability to inhibit the enzyme telomerase. Several N-acridyl maleimide (NAM), N-acridyl succinimide (NAS) and N-acridyl phthalimide (NAP) derivatives have been synthesized and evaluated for their anti cancer activity against various cancer cell lines. While synthesizing acridine derivatives it was required to form the C-N bonds at various stages. Developed a copper-nicotinic acid complex, which catalyzes the coupling of aryl halides with N-formyl amines and cyclic imides to form C-N bond. Explored Cu (II) catalyzed formation of C-N bond by coupling aryl halides with various N-nucleophiles such as formamide, N,N-dimethyl formamide, N-formyl amines and various cyclic imides.

DNA nanotechnology has been developed in order to construct nanostructures and nanomachines by virtue of the programmable self-assembly properties of DNA molecules. Although DNA nanotechnology initially focused on spatial arrangement of DNA strands, new horizons have been explored owing to the development of the toehold-mediated strand-displacement reaction, conferring new dynamic properties to previously static and rigid structures. A large variety of DNA reconfigurable nanostructures, stepped and autonomous nanomachines and circuits have been operated using the strand-displacement reaction. Biological systems rely on information processing to guide their behaviour and functions. Molecular computation is a branch of DNA nanotechnology that aims to construct and operate programmable computing devices made out of DNA that could interact in a biological context. Similar to conventional computers, the computational processes involved are based on Boolean logic, a propositional language that describes statements as being true or false while connecting them with logic operators. Numerous logic gates and circuits have been built with DNA that demonstrate information processing at the molecular level. However, development of new systems is called for in order to perform new tasks of higher computational complexity and enhanced reliability. The contribution of secondary structure to the vulnerability of a toehold-sequestered device to undesired triggering of inputs was examined, giving new approaches for minimizing leakage of DNA devices. This device was then integrated as a logic component in a DNA-based computer with a retrievable memory, thus implementing two essential biological functions in one synthetic device. Additionally, G-quadruplex logic gates were developed that can be switched between two topological states in a logic fashion. Their individual responses were detected simultaneously, establishing a new approach for parallel biological computing. A new AND-NOT logic circuit based on the seesaw mechanism was constructed that, in combination with the already existing AND and OR gates, form a now complete basis set that could perform any Boolean computation. This work introduces a new mode of kinetic control over the operation of such DNA circuits. Finally, the first example of a transmembrane logic gate being operated at the single-molecule level is described. This could be used as a potential platform for biosensing.

G-quadruplexes are non-canonical nucleic acid secondary structures of increasing biological and medicinal interest due to their proposed physiological functions in transcription, replication, translation and telomere biology. Aberrant G4 formation and stabilisation have been linked to genome instability, cancer and other diseases. However, the specific genes and pathways involved are largely unknown, and the work within this thesis aims to investigate this. Stabilisation of G4s by small molecules can perturb G4-mediated processes and initial studies suggest that this approach has chemotherapeutic potential. I therefore also aimed to identify cell genotypes sensitive to G4-ligand treatment that may offer further therapeutic opportunities. To address these aims, I present the first unbiased genome-wide genetic screen in cells where genes were silenced via short-hairpin RNAs (shRNAs) whilst being treated with either PDS or PhenDC3, two independent G4-stabilising small molecules. I explored gene deficiencies that enhance cell death (sensitisation) or provide a growth advantage (resistance) in the presence of these G4-ligands. Additionally, I present a validation screen, comprising hits uncovered via genome-wide screening, and also the use of this in another cell line of different origin. Sensitivities were enriched in DNA replication, cell cycle, DNA damage repair, splicing and ubiquitin-mediated proteolysis proteins and pathways. Ultimately, I uncovered four synthetic lethalities BRCA1, TOP1, DDX42, GAR1, independent of cell line and ligand. These were validated with three G4-stabilising ligands (PDS, PhenDC3 and CX-5461) using an independent siRNA approach. The latter siRNA methodology was used to screen 12 PDS derivatives with improved medicinal chemistry properties and ultimately identified SA-100-128, as a lead compound. The mechanism behind synthetic lethality with G4-stabilising ligands was explored further for DDX42, which I show has in vitro affinity for both RNA- and DNA-G4s and may represent a previously unknown G4-helicase. Also within this thesis, gene deficiencies that provided a growth advantage to PDS and/or PhenDC3 as uncovered by genome-wide and focused screening were explored. These showed enrichment in transcription, chromatin and lysosome-associated genes. The resistance phenotype of three gene deficiencies, TAF1, DDX39A and ZNF217 was further supported by additional siRNA experiments. Overall, I satisfied the primary aims and established many novel synthetic lethal and resistance interactions that may represent new therapeutic possibilities. Additionally, the results expand our knowledge of G4-biology by identifying genes, functions and subcellular locations previously not known to involve or regulate G4s.

Le glioblastome multiforme (GBM) est une tumeur cérébrale extrêmement agressive associée à un mauvais pronostic. C'est pourquoi, il apparaît nécessaire d'identifier les mécanismes moléculaires participant au développement des GBM ainsi qu'à leurs résistances aux traitements afin de développer de nouvelles approches thérapeutiques. Récemment, il a été montré que les régulations traductionnelles jouent un rôle fondamental dans les propriétés agressives du GBM. Les protéines de liaison à l'ARN (RBP) sont des acteurs majeurs de ces régulations dont l'expression/activité est altérée dans les GBM. Les RBP hnRNP HF (HF) font partie des RBP les plus surexprimées dans les GBM et leur contribution dans la régulation traductionnelle des GBM n'a encore jamais été investiguée. Nous avons émis l'hypothèse que hnRNP H et hnRNP F soient au centre d'un réseau de régulations post-transcriptionnelles impactant la machinerie traductionnelle qui contrôle le développement tumoral et la résistance aux traitements des GBM. Nos résultats montrent qu'HF régulent la prolifération et la réponse aux traitements car leur perte d'expression (i) diminue la prolifération des GBM (modèle cellulaire, sphéroïde et xénogreffes in vivo), (ii) active les voies de réponse aux dommages à l'ADN et (iii) sensibilise les cellules de GBM aux irradiations. De plus, nous avons identifié un nouveau rôle pour HF en tant que régulateurs de la traduction. En effet, nos données montrent que les hnRNP HF contrôlent la traduction d'un ensemble d'ARNm en régulant l'expression et l'activité de facteurs d'initiation ainsi qu'en collaborant avec des ARN hélicases partenaires en ciblant des ARNm impliqués dans des processus reliés au développement tumoral et la résistance aux traitements possédant des structures secondaires G-quadruplexe dans leurs 5'UTR. Les données que nous avons générées suggèrent que hnRNP H et hnRNP F sont des régulateurs traductionnels essentiels au développement tumoral et à la résistance aux traitements des GBM. / Glioblastoma multiforme (GBM) is one of the most aggressive brain tumors with poor prognosis. Understanding the molecular mechanisms involved in the development and resistance to treatments of gliomas could improve treatment efficiency. Recently, it has been demonstrated that translational regulations play a key role in the GBM aggressivity. RNA binding proteins (RBP) are major regulators of these processes and have altered expression / activity in GBM. The RBP hnRNP H and hnRNP F (HF) are among the most overexpressed RBP in GBM and their role in GBM translational regulation has never been investigated yet. We hypothesize that HF are at the core of a post-transcriptional regulation network which impacts the translational machinery that controls GBM tumor development and resistance to treatment. We have demonstrated that hnRNP H and hnRNP F regulate proliferation and response to treatment because their depletion (i) decreases the GBM proliferation (cell line model, spheroid and in vivo xenografts), (ii) activates the DNA damage response pathways and (iii) sensitizes the GBM cells to irradiation. We have identified HF as new regulators of GBM translation. Indeed, our data show that hnRNP H and hnRNP F control mRNA translation by regulating expression/activity of initiation factors and in collaboration with RNA helicases by targeting mRNA involved in oncogenic processes and containing secondary structures called G-quadruplex in their 5'UTR. The data that we have generated suggest that HF are essential translational regulators involved in tumor development and resistance to treatment in GBM.