Les oligonucléotides (ONs) antisens présentent un fort potentiel en tant qu’agents thérapeutiques. Toutefois, leurs propriétés physicochimiques limitent leur utilisation en thérapie génique. Pour pallier aux divers obstacles, des systèmes de vectorisation, tels que les micelles polyioniques (PICMs), ont été développés. Grâce à leur structure unique, les micelles protégent l’ON contre une dégradation prématurée et le couplage d’un ligand à leur surface augmente leur spécificité et leur internalisation. Dans d’autres systèmes, un polymère adjuvant aux propriétés pH-sensibles peut être ajouté pour faciliter la sortie de l’endosome et augmenter l’efficacité de l’ON. L’objectif général de ce mémoire était de mettre au point des PICMs ternaires ciblées pour l’administration d’ONs. Ces micelles assureraient à la fois l’internalisation cellulaire de leur cargaison en interagissant avec des récepteurs cellulaires et sa fuite de l’endosome grâce à un mécanisme de déstabilisation de la membrane endosomale. Pour cela, des PICMs composées d’un copolymère cationique de type poly(éthylène glycol)-bloc-poly(méthacrylate d’(alkylamino)éthyle) et d’un copolymère d’acide méthacrylique ont été préparées. Les propriétés physicochimiques de ces vecteurs ont démontré qu’ils permettaient une condensation efficace de l’acide nucléique et ce, indépendamment de la nature du polymère cationique et de l’acide nucléique. Finalement, une approche de couplage par pont disulfure a été développée afin de greffer au copolymère un fragment d’anticorps dirigé contre les récepteurs de la transferrine. En conclusion, ces travaux démontrent la versatilité et le potentiel des PICMs ternaires en tant que vecteurs d’acide nucléique, et proposent une méthodologie de couplage d’un ligand afin de formuler des PICMs ciblées. / Antisens oligonucleotides (ONs) present great potential as therapeutic agents. However, their physicochemical properties hinder their use in gene therapy. Targeting systems, such as polyion complex micelles (PICMs), have been proposed to circumvent the main hurdles related to ON delivery. Their unique core/shell structure can protect the ON against premature degradation and the coupling of a ligand on their surface can increase their specificity and internalization. In other systems, a polymer with pH-sensitive properties can be added to facilitate the release of the ON from the endosome and increase its efficiency. The present work was aimed at optimizing ternary PICMs targeted for the delivery of antisens ON. Such systems would provide both cellular internalization of cargo by interaction with receptors on the surface of cell membranes and escape from the endosome through a mechanism of destabilization of the endosomal membrane. PICMs composed of cationic copolymers of poly(ethylene glycol)-bloc-poly((alkylamino)ethyl methacrylate) with a methacrylic acid copolymer adjuvant were prepared. Their physicochemical properties suggest that efficient complexation of nucleic acids was obtained, regardless of the nature of the cationic polymer and the nature of the nucleic acid. Finally, a synthetic approach was developed for the conjugation of an antibody fragment directed against the transferrin receptor via a labile disulfide bond at the end of the cationic copolymer. In conclusion, the work presented herein displays the versatility and potential of ternary PICMs as vehicles for the delivery of ONs and also provides a method for the conjugation of a ligand to generate targeted ternary PICMs.

La Tomographie par émission de positons (TEP) constitue l’une des techniques d’imagerie médicale les plus novatrices pour la visualisation in vivo des processus biologiques. Elle intervient comme technique de choix pour le diagnostic dans de nombreux domaines notamment, en oncologie, cardiologie ou encore en neurologie. La conception et l’élaboration de nouveaux radiotraceurs sont en perpétuel développement. L’utilisationd’oligonucléotides (ODN) modifiés (aptamères) possédant une grande affinité et spécificité pour une cible (gène,protéine, principe actif), comme radiotraceur pour l’imagerie in vivo apparait comme une alternative intéressante. A ce jour, quelques rares exemples d’oligonucléotides marqués, par un radioisotope, ont été décrits dans la littérature.Dans ce contexte, il a été développé deux méthodologies d’introduction du radioisotope (11C ou 18F) en dernièreétape de synthèse par chimie ‘‘click’’ pour le marquage de nucléosides et d’oligonucléotides envisagés commeradiotraceurs pour la TEP. / Positron Emission Tomography (PET) is a powerful molecular-imaging technique for physiological and biologicalinvestigations in various areas, such as oncology, cardiology, and neurosciences, as well as for drug development.Due to the increasing need of this technique for in vivo applications, there is always a demand for the developmentof new tracers and radiolabeling strategies. Furthermore, because of their excellent targeting capacities and easysynthesis along with a high level of diversity, oligonucleotides are already extensively used in vitro as ligands fornucleic acids (antisense oligonucleotides), proteins, and small related molecules (aptamer oligonucleotides). Theuse of aptamers for in vivo imaging appears especially promising, because of the wide range of possibilitiesavailable to introduce variations in their structure through defined chemical modifications. However, only fewexamples of oligonucleotide labeling for PET have been reported. In this context, we have developed twomethodological ways to introduce the radioisotope (11C, 18F), by ‘‘click’’ chemistry, at the last radiosynthesis stepin order to label nucleoside and oligonucleotide as potential radiotracers for PET.

Die Telomere sind spezialisierte DNA-Protein-Komplexe, die sich an den Enden der Chromosomen der eukaryotischen Zellen befinden. Die Telomerase ist ein Ribonukleoprotein, welches für die vollständige Replikation der Telomere bei den meisten Eukaryoten verantwortlich ist. Die katalytische Untereinheit des Enzyms (hTERT beim Menschen) besitzt Reverse-Transkriptase-Aktivität, und nutzt eine integrierte RNA (hTR beim Menschen) als Template, um Telomer-Wiederholungssequenzen an den Enden der Chromosomen zu synthetisieren. Die Telomerase ist in den meisten normalen humanen somatischen Zellen unterdrückt. In den meisten Krebszellen jedoch, stellt die Reaktivierung der Telomerase zur Beibehaltung der Telomerlänge eine Voraussetzung für deren unbegrenztes Wachstumspotential dar. Im Rahmen dieser Arbeit sollte ein neuer, einfacher und selektiver Assay für den Nachweis der humanen Telomerase entwickelt werden. In dem neuen Assay sollten die beiden Kernkomponenten des Enzyms, die Protein-Untereinheit und die RNA, die Targets sein. Der Test ist in seiner Grundstruktur wie folgt aufgebaut : 1. Immobilisierung der Telomerase über die hTERT an eine Festphase, beschichtet mit Phosphorothioat-modifizierten (PS) Oligonukleotiden oder Heparin. Zusammen mit der Telomerase werden bei diesem Schritt die Heparin-bindenden Proteine, die in der Probe enthalten sind, an die Festphase gebunden. 2. Spezifischer Nachweis der hTR. Zur Detektion der hTR wird ein Oligonukleotid-Ligations-Assay (OLA) oder eine Reverse-Transkriptase-PCR (RT-PCR) eingesetzt. In der optimierten Endversion wurde zur Immobilisierung des Enzyms eine Festphase, beschichtet mit PS-Oligonukleotiden, verwendet. Die hTR wurde mittels RT-PCR nachgewiesen. Mit dem neuen Assay wurden erfolgreich 75 Tumorzellen detektiert. / Telomeres are specialized DNA-Protein structures located at the ends of linear eukaryotic chromosomes. Telomerase is a ribonucleoprotein, which is responsible for the complete replication of the telomeres in most eukaryotes. The catalytic reverse transcriptase protein subunit (hTERT in humans) of the nucleoprotein uses an integral RNA (hTR in humans) as a template for the addition of telomeric repeat sequences to the ends of chromosomes. Telomerase is repressed in most normal human somatic cells, while the reactivation of telomerase to maintain telomere length is necessary for the unlimited growth potential of most human cancer cells. The aim of this work was the development of a new, simple and selective assay for the detection of human telomerase. The targets of the new assay were the two core subunits of the enzyme : hTERT and hTR. The test comprises two principal steps : 1. Immobilization of the telomerase via the hTERT subunit on a solid phase, coated with heparin or phosphorothioate-modified (PS) oligonucleotides. In this step telomerase is bound together with the heparin-binding proteins of the analysed sample to the surface. 2. Specific detection of the hTR. For the detection of the hTR an oligonucleotide ligation assay (OLA) or a reverse transcriptase PCR (RT-PCR) was used. In the optimized final version of the assay a PS-coated solid phase was used for the immobilization of the enzyme. Reverse transcriptase PCR was applied for detection of the hTR. 75 tumor cells were successfully detected with the new assay.

This thesis is concerned with synthesis, structure and biochemical analysis of chemically modified oligonucleotides with potential therapeutic applications. The three types of chemical modifications described here are: (a) A North-East locked 1',2'-azetidine nucleoside (b) A North locked 2',4'-cyanomethylene bridged nucleoside and (c) A 2',4'-aza-ENA-T nucleoside. The synthesis of the 1',2'-azetidine fused nucleosides was described using two different approaches. A highly strained 2',4'-cyanomethylene locked nucleoside was synthesized but could not be converted to the phosphoramidite derivative due to instability during derivatization. The key cyclization step in the aza-ENA-T nucleoside synthesis gave rise to two separable diastereomers due to chirality at the exocyclic nitrogen. Conversion of diastereomer 55 to 56 occurred with a large free energy of activation (ΔG‡ = 23.4 kcal mol-1 at 298 K in pyridine-d5). Of the two isomers the equatorial NH product was more stable than the axial one due to reduced 1,3 diaxial interactions. As a result, all NH axial product was converted to the equatorial isomer during subsequent steps in the synthesis. NMR and ab initio experiments confirmed the North-East structure of the 1',2'-azetidine locked nucleoside and North conformation of aza-ENA-T locked nucleosides with a chair conformation of the piperidine ring. The amino modified nucleosides were incorporated into different positions of a 15mer oligonucleotide. The azetidine modified AONs did not form stable duplexes with complementary RNA (ΔTm ~-1 to -4 °C), but they performed better than previously synthesized isosequential 1',2'-oxetane modified oligonucleotides. The 2',4'-aza-ENA-T modified oligonucleotide, on the other hand, showed excellent target affinity with complementary RNA (ΔTm ~+4 °C). The azetidine and aza-ENA-T modified oligonucleotides showed significant stability in the presence of human serum and snake venom phosphodiesterase (3'-exonuclease) as compared to the unmodified native sequence. The singly modified 15mer oligonucleotides were also subjected to RNase H promoted digestion in order to evaluate their potential as effective antisense agents. The effective enzyme activity (kcat/Km) was found to be lower in the modified AONs due to reduced enzyme-substrate binding. However, the catalytic activity of RNase H with these modified-AON:RNA duplexes were higher than observed with the native duplex.

This thesis is based on six original research publications describing synthesis, structure and physicochemical and biochemical analysis of chemically modified oligonucleotides (ONs) in terms of their potential diagnostic and therapeutic applications. Synthesis of two types of bicyclic conformationally constrained nucleosides, North-East locked 1',2'-azetidine and North locked 2',4'-aza-ENA, is described. Study of the molecular structures and dynamics of bicyclic nucleosides showed that depending upon the type of fused system they fall into two distinct categories with their respective internal dynamics and type of sugar conformation. The physicochemical properties of the nucleobases in the conformationally constrained nucleosides found to be depended on the site and ring-size of the fused system. The incorporation of azetidine modified nucleotide units into 15mer ONs lowered the affinity toward the complementary RNA. However, they performed better than previously reported isosequential 1',2'-oxetane modified analogues. Whereas aza-ENA-T modification incorporated into ONs significantly enhanced affinity to the complementary RNA. To evaluate the antisense potential of azetidine-T and aza-ENA-T modified ONs, they were subjected to RNase H promoted cleavage as well as tested towards nucleolytic degradation. Kinetic experiments showed that modified ONs recruit RNase H, however with lower enzyme efficiency due to decreased enzyme-substrate binding affinity, but with enhanced turnover number. Both, azetidine-T and aza-ENA-T modified ONs demonstrated improved 3'-exonuclease stability in the presence of snake venom phosphodiesterase and human serum compared to the unmodified sequence. Oligodeoxynucleotides (ODNs) containing pyrene-functionalized azetidine-T (Aze-pyr X) and aza-ENA-T (Aza-ENA-pyr Y) modifications showed different fluorescence properties. The X modified ODNs hybridized to the complementary DNA and RNA showed variable increase in the fluorescence intensity depending upon the nearest-neighbor at the 3'-end to X modification (dA > dG > dT > dC) with high fluorescence quantum yield. However, the Y modified ODNs showed a sensible enhancement of the fluorescence intensity only with complementary DNA. Also, the X modified ODN showed decrease (~37-fold) in the fluorescence intensity upon duplex formation with RNA containing a G nucleobase mismatch opposite to the modification site, whereas a ~3-fold increase was observed for the Y modified probe.

The recent explosion of DNA sequence information has provided compelling evidence for the following facts. (1) Simple repetitive sequences-microsatellites and minisatellites occur commonly in the human genome and (2) these repetitive DNA sequences could play an important role in the regulation of various genetic processes including modulation of gene expression. These sequences exhibit extensive polymorphism in both length and the composition between species and between organisms of the same species and even cells of the same organism. The repetitive DNA sequences also exhibit structural polymorphism depending on the sequence composition. The functional significance of repetitive DNA is a well-established fact. The work done in many laboratories including ours has conclusively documented the functional role played by repetitive sequences in various cellular processes. Structural studies have established the sequence requirement for various non-B DNA structures and the functional significance of these unusual DNA structures is becoming increasingly clear. The structures that were characterised earlier purely from conformation point of view have aroused interest after the recent realisation that these structures could be formed in vivo when cloned in a supercoiled plasmid. The discovery of novel type of dynamic mutations where intragenic amplifications of trinucleotide repeats is associated with phenotypic changes causing many neurodegenerative disorders has provided the most compelling evidence for the importance of simple repeats in the etiology of these disorders. Secondary structures adopted by these simple repeats is a common causative factor in the mechanism of expansion of these repeats. This realisation prompted many investigations into the relationship between the DNA sequence, structure and molecular basis of dynamic mutation. Many experimental evidences have implicated paranemic DNA structures in various biological processes, especially in the regulation of gene expression. Earlier work done in our laboratory on the structure function relationship of repetitive DNA sequences provided experimental evidence for the role of paranemic DNA structure in the regulation of gene expression. It was demonstrated that intramolecular triplex potential sequences within a gene downregulate its expression in vivo (Sarkar and Brahmachari (1992) Nucleic Acids Res., 20, 5713-5718). Similarly the effect of cruciform structure forming sequences on gene expression was also documented. Sequence specific alterations in DNA structures were studied in our laboratory using a variety of biophysical and biochemical techniques. An intramolecular, antiparallel tetraplex structure was proposed for human telomeric repeat sequences (Balagurumoorthy, et al., (1994) J. Biol. Chem., 269, 21858-21869). The telomeric repeats are not only present at the end of chromosomes but they are also present at many interstitial sites in the human genome. Database search reveals that the human telomeric sequences as well as similar sequences with minor variations are present at many locations in the human genome. Telomeric repeats are GC rich sequences with the G rich strand protruding as a 3' end overhang at the end of chromosomes. When human telomeric repeats are cloned in a supercoiled plasmid, the C rich strand adopts a hairpin like conformation where as the G-rich strand extrudes into a quadruplex structure. However, the biological significance of these structures in vivo still remains to be elucidated completely. The role of a putative tetraplex DNA structure in the insulin gene linked polymorphic region of the human insulin gene in vivo in the regulation of expression of the insulin gene has been suggested. In this context, we have addressed the question whether the telomeric repeats when present within a gene affect its expression in vivol If so, what would be the possible mechanism? An attempt has been made to understand the effect of presence of telomeric repeats within a gene on its expression. The details of these studies have been presented in Chapter 2 of this thesis. Contrary to telomeric repeats which provide stability to the chromosomes, recently expansion of a GC rich dodecamer repeat upstream of cystatin B gene (chromosome 21q) has been shown to be the most common mutation associated with Progressive Myoclonus Epilepsy (EPM1) of Unverricht-Lundberg type. Two to three copies of the repeat (CCCCGCCCCGCG)n are present in normal individuals whereas the affected individuals have 30-75 copies of this repeat. The expression of cystatin B gene is reduced in patients in a cell specific manner. The repeat also shows intergenerational variability. The exact mechanism of expansion of this repeat is not known. In the case of trinucleotide repeat expansion, it is shown that the structure adopted by the repeat plays an important role in the mechanism of expansion and that some of the secondary structures adopted by trinucleotide repeats could be inherently mutagenic conformations. In order to understand the mechanism of expansion EPM1 dodecamer repeat, the work reported in this thesis was carried out with the following objectives. • To understand the structure of G rich and C-rich strands of EPM1 repeat. • To understand the variations in the structure with the increase in the length and its possible implications in the mechanism of expansion of EPM 1 repeat. Studies aimed with these objectives are presented in chapters 3, 4 and 5 of the thesis. Chapter 1 provides a general introduction to repetitive DNA, the various structures adopted by repetitive DNA sequences in the genome, the functional significance of the various simple repetitive DNA sequences in the genome has been presented. An account of trinucleotide repeat expansion and associated disorders, non-trinucleotide repeat expansions and associated disorders has been presented. The various non B-DNA structures adopted these repeats and their implications in the mechanism of expansion have been discussed. Chapter 2 describes in frame cloning of human telomeric repeats d(G3T2A)3G3 in the N-terminal region of β-galactosidase gene. The effect of such repeat Sequences on transcription elongation in vivo has been studied using E.coli as a model system. The 3.5 copies of human telomeric repeat sequences were cloned in the sense strand of plasmid pBluescriptllSK+ so as to create plasmid clone pSBQ8 and in the template strand of plasmid pBluescriptHKS+ so as to create clone pSBRQ8. One dimensional chloroquine gel shift assay indicated presence of an unwound structure in pSBQ8 and pSBRQ8. β-galactosidase activity assay suggested downregulation of the gene in vivo. In the case of plasmid pSBQ8 the difference in β-galactosidase activity was approximately 6 fold as compared to the parent plasmid pBluescriptIISK+ whereas in the case of pSBRQ8 the difference in β-galactosidase activity was approximately 8 fold as compared to the control pBluescriptIIKS+. The analysis of β-galactosidase transcript showed that full length transcript was formed in the case of pSBQ8. Full length transcript was not formed in the case of pSBRQ8. We propose that in the case of pSBQ8 the gene expression is inhibited in steps subsequent to transcription elongation. In the case of pSBRQ8, we propose that quadruplex structure may be formed by the template strand at the DNA level thereby blocking transcription elongation step. Chapter 3 describes studies aimed at understanding the structure of G-rich strand (referred to as G strand) of Progressive Myoclonus Epilepsy (EPM1) repeat. The sequence of the G strand of dodecamer EPM1 repeat is d(GGGGCGGGGCGC)n. Oligoucleotides containing one (12mer), two (24mer) and three(36mer) were synthesised. These oligonucleotides are referred to as dG12, dG24 and dG36 respectively. Structural studies were carried out using CD spectroscopy, UV melting, non-denaturing gel electrophoresis and chemical and enzymatic probing. The G strand oligonucleotides showed enhanced gel elecrophoretic mobility in the presence of monovalent cations KCl and NaCl. Oligonucleotide dG12 also showed retarded species on non-denaturing gel in the presence of 70mM KCl indicating intermolecular associations. Oligonucleotides dG24 and dG36 predominantly formed intramolecular structures which migrated anomalously faster than the expected size. The CD spectrum for dG12 showed an intense positive band at 260nm and a negative band at 240nm in the presence of KCl indicative of an intermolecular, parallel G quartet structure. The CD spectra of dG24 and dG36 showed 260nm positive peak, 240nm negative peak along with a positive band around 290nm. This is indicative of folded back structure. These findings support the results of non-denaturing gel electrophoresis of G strand oligonucleotides. The UV melting profiles suggested increase in the stability with the increase in the length. These structures were further characterised by PI nuclease and chemical probing using DMS and DEPC. The structural studies with G-rich strand of EPM1 dodecamer repeat showed that this repeat motif adopts intramolecularly folded structures with increase in the length of the repeat thereby favouring slippage during replication. Chapter 4 deals with the studies aimed at understanding the structure at acidic pH of C-rich strand (referred to as C strand) of Progressive Myoclonus Epilepsy (EPM1) repeat. The sequence of the C strand of dodecamer EPM1 repeat is d(CCCCGCCCCGCG)n. The C rich oligonucleotides are known to form a four stranded structure called i-motif at acidic pH involving intercalated base pairs. The i-motif consists of two parallel stranded, base paired duplexes are arranged in an antiparallel orientation. Since, the base pairs of one base paired duplex intercalate into those of the other duplex, the structure is called as i-motif. We have investigated structure of C strand of EPM1 repeat by circular dichroism (CD), native polyacrylamide gel electrophoresis and UV melting. Oligonucleotide dC12 showed two bands of which the major band was retarded on the native gel (pH 5.0) at low temperature suggesting that dC12 predominantly formed intermolecular structure, Oligonucleotides dC24 and dC36 migrated anomalously faster than the expected size indicating formation of compact, intramolecularly folded structures. Circular dichroism studies indicate that, all the oligonucleotides displayed an intense positive band near 285nm, a negative band around 260nm with a cross over at 270nm, This is a characteristic CD signature for an i-motif structure and reflects the presence of secondary structure due to formation of hydrogen bonded pairs between protonated cytosines. All the C strand oligonucleotides showed hyperchromism at 265nm, which is an isobestic wavelength for C protonation. Studies described in this chapter suggest an intramolecular i-motif structure for dC24 and dC36 and an intermolecular i-motif for oligonucleotide dC12. In addition, it was interesting to note that inspite of the presence of G residues, the stretch of C residues could adopt i-motif structure. Although these structures are formed at an acidic pH, it is indicative of formation of possible intramolecularly folded structure. Many reports have suggested the possibility of cytosine rich sequences adopting i-motif structure even at neutral pH. In order to test this possibility, structural studies were carried out on the C strand EPM1 oligonucleotides at pH 7.2 in the presence of 70mM NaCl. These studies have been described in Chapter 5. The investigations were done using CD spectroscopy, UV melting, native polyacrylamide gel electrophoresis, and chemical probing using hydroxylamine and PI nuclease. These studies indicate that all the C strand oligonucleotides form intramolecular, hairpin structure at physiological pH. All the three C strand oligonucleotides migrated anomalously faster on the native gel indicating the presence of a compact structure. The CD spectra at pH 7.2 showed a blue shift as compared to those at pH 5.0. This indicated absence of base pairs. The hydroxylamine chemical probing suggested presence of G-C Watson-Crick base pairs. The loop residues of the folded back hairpin structures were probed with PI nuclease. The C strand oligonucleotides showed possibility of formation of multiple hairpin structures with the increase in the length of the repeat. The propensity to form hairpin structures suggests a possibility of formation of slip loop structures during the replication process thereby promoting expansion of this repeat. Formation of folded back hairpin like structures is significant in terms of mechanism of expansion of this repeat. Chapter 6 is devoted to concluding remarks highlighting the significance of the experimental results presented in this thesis and their possible biological implications in the light of contemporary research.

A significant focus of toxicological research is the identification of electrophiles that covalently modify DNA to form addition products (adducts). These products can be generated when aryl radical species react at the C8-site of 2'-deoxyguanosine (dG) to form C8-aryl-dG adducts, which are mutagenic lesions. While this form of DNA modification is detrimental, C8-aryl-dG adducts also possess intriguing properties that can be exploited for beneficial purposes. This thesis is an investigation of one mechanism believed to contribute to the mutagenicity of C8-aryl-dG adducts, as well as a study of the photophysical properties of adducts that allow for their application as fluorescent probes. A common property of C8-aryl-dG adduction is accompaniment of abasic site formation. To determine how the C8-aryl moiety contributes to sugar loss, UV-Vis spectroscopy has been employed to determine hydrolysis kinetics, with C8-aryl-dG adducts found to be more prone than dG to acid-catalyzed hydrolysis. Despite adduct reactivity in acidic media, all adducts are relatively stable at pH 7, suggesting they are unlikely intermediates of abasic site formation at physiological pH. These results have allowed for development of a new rationale for depurination observed upon C8-aryl-dG adduction within duplex DNA. The determination of photophysical parameters of C8-heteroaryl-dG adducts reveals that these nucleosides behave as fluorophores with high fluorescence quantum yields (φfl). These adducts also exhibit emission sensitivity to their solvent environment and H-bonding interactions. C8-Heteroaryl-dG adducts were incorporated in the oligonucleotide 5'-CTCG1G2CG3CCATC, at the G1 and G3 sites, that contains the recognition sequence of the NarI Type II restriction enzyme. Hybridization of the modified NarI oligonucleotides to the complementary strand containing either the C or G nucleobase opposite the adduct allowed for characterization of duplex structures by circular dichroism (CD), UV melting temperature analysis and fluorescence spectroscopy. Results suggest that the C8-heteroaryl-dG adduct favours an anti conformation with base-paired with C, while a syn conformation is favoured when base-paired to G. Adduct conformation of bulky C8-dG adducts is believed to be correlated with their known mutagenic activity. C8-Heteroaryl-dG modified nucleosides could therefore be used as fluorescent models of these adducts to aid in elucidation of adduct-induced mutagenesis in biological systems. / NSERC

Les oligonucléotides (ONs) antisens présentent un fort potentiel en tant qu’agents thérapeutiques. Toutefois, leurs propriétés physicochimiques limitent leur utilisation en thérapie génique. Pour pallier aux divers obstacles, des systèmes de vectorisation, tels que les micelles polyioniques (PICMs), ont été développés. Grâce à leur structure unique, les micelles protégent l’ON contre une dégradation prématurée et le couplage d’un ligand à leur surface augmente leur spécificité et leur internalisation. Dans d’autres systèmes, un polymère adjuvant aux propriétés pH-sensibles peut être ajouté pour faciliter la sortie de l’endosome et augmenter l’efficacité de l’ON. L’objectif général de ce mémoire était de mettre au point des PICMs ternaires ciblées pour l’administration d’ONs. Ces micelles assureraient à la fois l’internalisation cellulaire de leur cargaison en interagissant avec des récepteurs cellulaires et sa fuite de l’endosome grâce à un mécanisme de déstabilisation de la membrane endosomale. Pour cela, des PICMs composées d’un copolymère cationique de type poly(éthylène glycol)-bloc-poly(méthacrylate d’(alkylamino)éthyle) et d’un copolymère d’acide méthacrylique ont été préparées. Les propriétés physicochimiques de ces vecteurs ont démontré qu’ils permettaient une condensation efficace de l’acide nucléique et ce, indépendamment de la nature du polymère cationique et de l’acide nucléique. Finalement, une approche de couplage par pont disulfure a été développée afin de greffer au copolymère un fragment d’anticorps dirigé contre les récepteurs de la transferrine. En conclusion, ces travaux démontrent la versatilité et le potentiel des PICMs ternaires en tant que vecteurs d’acide nucléique, et proposent une méthodologie de couplage d’un ligand afin de formuler des PICMs ciblées. / Antisens oligonucleotides (ONs) present great potential as therapeutic agents. However, their physicochemical properties hinder their use in gene therapy. Targeting systems, such as polyion complex micelles (PICMs), have been proposed to circumvent the main hurdles related to ON delivery. Their unique core/shell structure can protect the ON against premature degradation and the coupling of a ligand on their surface can increase their specificity and internalization. In other systems, a polymer with pH-sensitive properties can be added to facilitate the release of the ON from the endosome and increase its efficiency. The present work was aimed at optimizing ternary PICMs targeted for the delivery of antisens ON. Such systems would provide both cellular internalization of cargo by interaction with receptors on the surface of cell membranes and escape from the endosome through a mechanism of destabilization of the endosomal membrane. PICMs composed of cationic copolymers of poly(ethylene glycol)-bloc-poly((alkylamino)ethyl methacrylate) with a methacrylic acid copolymer adjuvant were prepared. Their physicochemical properties suggest that efficient complexation of nucleic acids was obtained, regardless of the nature of the cationic polymer and the nature of the nucleic acid. Finally, a synthetic approach was developed for the conjugation of an antibody fragment directed against the transferrin receptor via a labile disulfide bond at the end of the cationic copolymer. In conclusion, the work presented herein displays the versatility and potential of ternary PICMs as vehicles for the delivery of ONs and also provides a method for the conjugation of a ligand to generate targeted ternary PICMs.

Les défauts de génome mitochondrial provoquent des maladies neuromusculaires, pour lequel aucun traitement efficace n'a été mis au point. La plupart des mutations mitochondriales sont hétéroplasmique, ce qui signifie que l'ADN mitochondrial (ADNmt) de type sauvage et muté coexistent dans la même cellule, et le changement de proportion entre deux types d'ADNmt pourrait rétablir les fonctions mitochondriales. Le but du projet était le développement du système pour cibler l'ARN thérapeutique dans les cellules humaines vivantes. Au cours de ma thèse j'ai synthétisé une série de nouveaux ARN anti-réplicatifs contenant modifications chimiques pour augmenter leur stabilité dans la cellule, et mis au point la nouvelle méthode de synthèse chimique des molécules d'ARN contenant cholestérol fixé par l'intermédiaire d'un pont biodégradable. Ces ARN étaient capable de pénétrer dans les cellules humains, d'être adressées dans les mitochondries et de diminuer la proportion d' ADNmt muté. / Defects in mitochondrial genome cause neuromuscular diseases, for which no efficient therapy has been developed. Since most mitochondrial mutations are heteroplasmic, wild type and mutated mitochondrial DNA (mtDNA) coexist in the same cell, and the shift in proportion between two mtDNA types could restore mitochondrial functions. The aim of the project was development of carrier-free system for targeting the therapeutic mitochondrially importable RNA into living human cells. During my PhD study, I have synthesized a set of new anti-replicative RNAs containing various chemical modifications, aiming to increase their stability in the cell, and developed a new method for the chemical synthesis of RNA molecules containing cholesterol attached through a biodegradable bridge. Cholesterol containing antireplicative RNAs were characterised by efficient cellular uptake, partial colocalisation with mitochondria and ability to decrease the proportion of mutant mtDNA.

Le couplage de Stille modifié développé par l’équipe du Pr Fouquet a été appliqué à la méthylation de nucléosides, dinucléotides et oligonucléotides dans le but de mettre au point une méthodologie de marquage d’aptamères au carbone 11 pour le diagnostic précoce de cancer par TEP. Ce couplage pallado-catalysé est basé sur l’utilisation de monoorganoétain activé par une source de fluorure permettant d’accélérer la réaction. Dans un premier temps, les essais méthodologiques ont permis de mettre au point le transfert de groupement méthyle sur différents nucléosides et un dinucléotide modifiés dans des conditions compatibles avec la durée de demi-vie du carbone 11 (20,4 min) et la nature particulière des oligonucléotides. Puis, cette méthodologie a été appliquée à des oligonucléotides modèles obtenus après incorporation des nucléosides les plus prometteurs. / The modified Stille cross-coupling developed by Pr. Fouquet’s group was applied to the methylation of nucleosides, dinucleotides and oligonucleotides in order to develop a methodology for labelling aptamers with carbon 11 for the early diagnosis of cancer by PET. This pallado-catalyzed cross-coupling is based on the use of monoorganotin activated by a source of fluoride accelerating the reaction. Initial methodology tests helped to finalize the transfer of methyl group on various nucleosides and a dinucleotide, with reaction conditions compatible with the short half-life of carbon 11 (20.4 min) and the special nature of oligonucleotides. Then, this methodology was applied to oligonucleotide models obtained after incorporation of the most promising nucleosides.