L'une des stratégies mise en œuvre pour améliorer la prise en charge thérapeutique des patients concerne le développement d'outils diagnostiques sensibles et spécifiques. Les aptamères sont des oligonucléotides artificiels obtenus par SELEX avec une très haute affinité ainsi qu'une excellente spécificité pour leurs cibles. L'immobilisation de ces motifs de reconnaissance moléculaire à la surface de nanomatériaux tels que des nanoparticules d'or (AuNPs), dont les propriétés optiques et électroniques sont uniques, permet d'amplifier le signal généré par l'interaction du ligand avec sa cible. Deux systèmes de biosensing ont été élaboré en fonctionnalisant des AuNPs avec des aptamères, l'un dirigé contre la thrombine et le second dirigé contre une marque épigénétique portée par une protéine histone. La réduction des sels d'or aurique précurseurs a été réalisée en présence de PEG4 et a conduit à l'obtention d'une population homodisperse de AuNPs sphériques d'un diamètre moyen de 14 nm et présentant une isotropie de taille et de forme. Ces AuNPs ont ensuite été fonctionnalisées par des bras espaceurs de longueur variable constitués d'unités tétraéthylène glycol successives reliées entre elles par des ponts éthers ou triazoles. L'acide lipoique a été utilisé comme motif d'ancrage à la surface des AuNPs via une liaison covalente Au-S et a été couplé aux différents bras espaceurs via une réaction de Steglich. Les linkers étaient porteurs d'un groupement terminal azoture afin de réaliser le couplage par chimie-click avec les aptamères. La stratégie de détection de la thrombine utilisait les propriétés de quenching de fluorescence des AuNPs alors que la détection de l'histone était colorimétrique et mettait à profit l'effet de résonance plasmonique de surface des nanoparticules d'or. / Improving patients therapeutic care needs the development of sensitive and specific diagnostic tools. Aptamers are synthetic oligonucleotides obtained by SELEX with a very high affinity and excellent specificity for their targets. Grafting of these molecular recognition patterns onto nanomaterials such as gold nanoparticles (GNPs), which unique optical and electronic properties, can amplify the signal induce by the interaction between the ligand and its target. Two biosensing systems have been developed by GNP functionalization with aptamers, one is directed against thrombin and the second against an epigenetic mark carried by a histone protein. Gold precursors was reduced in the presence of PEO4 and led to a homodisperse population of spherical GNP with an average diameter of 14 nm and an isotropy of size and shape. GNP were functionalized with tetraethylene glycol units interconnected by ether or triazoles bridges as a linker. Lipoic acid was used as an anchor moiety onto gold surface via a covalent Au-S bond and was coupled to the spacer through a Steglich reaction. The linkers were functionalized with an azide group to perform the coupling with aptamers by click chemistry. The thrombin sensing strategy used the fluorescence quenching properties of GNPs while the histone detection involved the gold nanoparticle plasmon resonance surface effect.

PhD / SYNOPSIS OF THIS THESIS The aim of this thesis is to more fully understand and explain the binding mechanism of organic molecules to the Au(111) surface and to explore the conduction of such molecules. It consists of five discreet chapters connected to each other by the central theme of “The Single Molecule Device: Conductance and Binding”. There is a deliberate concentration on azine linkers, in particular those with a 1,10-phenanthroline-type bidentate configuration at each end. This linker unit is called a “molecular alligator clip” and is investigated as an alternative to the thiol linker unit more commonly used. Chapter 1 places the work in the broad context of Molecular Electronics and establishes the need for this research. In Chapter 2 the multiple break-junction technique (using a Scanning Tunnelling Microscope or similar device) was used to investigate the conductance of various molecules with azine linkers. A major finding of those experiments is that solvent interactions are a key factor in the conductance signal of particular molecules. Some solvents interfere with the molecule’s interaction with and attachment to the gold electrodes. One indicator of the degree of this interference is the extent of the enhancement or otherwise of the gold quantized conduction peak at 1.0 G0. Below 1.0 G0 a broad range for which the molecule enhances conduction indicates that solvent interactions contribute to a variety of structures which could bridge the electrodes, each with their own specific conductance value. The use of histograms with a Log10 scale for conductance proved useful for observing broad range features. vi Another factor which affects the conductance signal is the geometric alignment of the molecule (or the molecule-solvent structure) to the gold electrode, and the molecular alignment is explored in Chapters 3 for 1,10-phenanthroline (PHEN) and Chapter 4 for thiols. In Chapter 3 STM images, electrochemistry, and Density Functional Theory (DFT) are used to determine 1,10-phenanthroline (PHEN) structures on the Au(111) surface. It is established that PHEN binds in two modes, a physisorbed state and a chemisorbed state. The chemisorbed state is more stable and involves the extraction of gold from the bulk to form adatom-PHEN entities which are highly mobile on the gold surface. Surface pitting is viewed as evidential of the formation of the adatom-molecule entities. DFT calculations in this chapter were performed by Ante Bilic and Jeffery Reimers. The conclusions to Chapter 3 implicate the adatom as a binding mode of thiols to gold and this is explored in Chapter 4 by a timely review of nascent research in the field. The adatom motif is identified as the major binding structure for thiol terminated molecules to gold, using the explanation of surface pitting in Chapter 3 as major evidence and substantiated by emergent literature, both experimental and theoretical. Furthermore, the effect of this binding mode on conductance is explored and structures relevant to the break-junction experiment of Chapter 2 are identified and their conductance values compared. Finally, as a result of researching extensive reports of molecular conductance values, and having attempted the same, a simple method for predicting the conductance of single molecules is presented based upon the tunneling conductance formula.

Dans ce travail, nous avons étudié en détails l'interaction de l'histone H1 avec l'ADN nucléosomal afin de comprendre comment cette interaction conduit à l'organisation en fibre nucléosomale. Nous avons pu résoudre ce problème ancien par l'utilisation de : (i) l'incorporation de H1 par une chaperonne d'histone physiologique, NAP-1, (ii) la reconstitution de nucléosomes parfaitement homogènes sur une matrice d'ADN contenant la séquence 601 fortement positionnante, (iii) une combinaison de cryo-microscopie électronique (EC-M) et de technique d'empreinte aux radicaux OH°, (iv) une modélisation mécanique du polymère ADN de type « coarse-grain ». Notre « cartographie » par empreinte OH° de résolution d'un nucléotide montre que le domaine globulaire de H1 (GH1) interagit à travers le petit sillon avec des « patch » d'ADN de 10 pb de part et d'autre de la dyade du nucléosome. De plus, GH1 organise environ un tour d'hélice d'ADN de chaque ADN de liaison du nucléosome. En même temps, une suite de 7 acides aminés (120-127) de la partie COOH-terminale est requise pour la formation de la structure en tige de l'ADN de liaison.

Huntington’s disease (HD) is a neurodegenerative disorder caused by the inheritance of one mutant copy of the huntingtin gene. Mutant huntingtin protein (mHtt) contains an expanded polyglutamine repeat region near the N-terminus. Cleavage of mHtt releases an N-terminal fragment (N-mHtt) which translocates, and accumulates in the nucleus. Nuclear accumulation of N-mHtt has been directly associated with cellular toxicity. Decreased transcription is among the earliest detected changes that occur in the brains of HD patients and is consistently observed in all animal and cellular models of HD. Transcriptional dysregulation may trigger many of the perturbations that occur later in disease progression and an understanding of the effects of mHtt may lead to strategies to slow the progression of the disease. Current models of N-mHtt-mediated transcriptional dysregulation suggest that abnormal interactions between N-mHtt and transcription factors impair the ability of these transcription factors to associate at N-mHtt-affected promoters and properly regulate gene expression. We tested various aspects of these models using two N-mHtt-affected promoters in in vitro transcription assays and in two cell models of HD using techniques including overexpression of known N-mHtt-interacting transcription factors, chromatin immunoprecipitation, promoter deletion and mutation analyses and in vitro promoter binding assays. Based on our results and those in the literature, we proposed a new model of N-mHtt-mediated transcriptional dysregulation centered on the presence of N-mHtt at affected promoters. We concluded that simultaneous interaction of N-mHtt with multiple binding partners within the transcriptional machinery would explain the gene-specificity of N-mHtt-mediated transcriptional dysregulation, as well as the observation that some genes are affected early in disease progression while others are affected later. Our model explains why alleviating N-mHtt-mediated transcriptional dysregulation through overexpression of N-mHtt-interacting proteins has proven to be difficult and suggests that the most realistic strategy for restoring gene expression across the spectrum of N-mHtt affected genes is by reducing the amount of soluble nuclear N-mHtt.

This thesis gives a detailed description of the design and synthesis of new organic sensitizers for Dye sensitized Solar Cells (DSCs). It is divided in 7 chapters, where the first gives an introduction to the field of DSCs and the synthesis of organic sensitizers. Chapters 2 to 6 deal with the work of the author, starting with the first publication and the other following in chronological order. The thesis is completed with some concluding remarks (chapter 7). The DSC is a fairly new solar cell concept, also known as the Grätzel cell, after its inventor Michael Grätzel. It uses a dye (sensitizer) to capture the incident light. The dye is chemically connected to a porous layer of a wide band-gap semiconductor. The separation of light absorption and charge separation is different from the conventional Si-based solar cells. Therefore, it does not require the very high purity materials necessary for the Si-solar cells. This opens up the possibility of easier manufacturing for future large scale production. Since the groundbreaking work reported in 1991, the interest within the field has grown rapidly. Large companies have taken up their own research and new companies have started with their focus on the DSC. So far the highest solar energy to electricity conversion efficiencies have reached ~12%. The sensitizers in this thesis are based on triphenylamine or phenoxazine as the electron donating part in the molecule. A conjugated linker allows the electrons to flow from the donor to the acceptor, which will enable the electrons to inject into the semiconductor once they are excited. Changing the structure by introducing substituents, extending the conjugation and exchanging parts of the molecule, will influence the performance of the solar cell. By analyzing the performance, one can evaluate the importance of each component in the structure and thereby gain more insight into the complex nature of the dye sensitized solar cell. / QC 20110505

We did functional characterisation of Drosophila melanogaster linker histone, dH1. In the mutant state for this protein, we observed structural changes in polytene chromosomes chromocenter and nucleoli of mutant larvae. In addition, we performed a microarray analysis in H1 mutant background in order to determine contribution of dH1 to gene expression regulation. We determined effects of dH1 loss in different types of chromatin and we identified groups of differentially expressed (DE) genes, groups in sense of physical clusters of genes and genomic elements rather than groups of functionally related genes. We found that dH1 affects in greater extent expression of heterochromatin genes compared to its effect on euchromatin genes; that dH1 regulates transcription in a regional manner, since the genes physically nearest to the most DE genes tend to be upregulated as well; and that dH1 is negatively regulating expression of transposable elements and members of certain gene families. In addition, we found that dH1 is necessary for preserving genome stability. Among DE transposable elements we detected R1 and R2 retrotransposons, elements that are integrating specifically in rRNA locus. We showed that activation of their transcription is also upregulating expression of aberrant, transposon-inserted, rDNA units of the locus. In this regard we observed an accumulation of extra-chromosomal rDNA circles, increased γ-H2Av content, stop in cell proliferation and activation of apoptosis. Altogether, these results are revealing so far unknown role of histone H1 in preserving genome stability and its effects on cell proliferation.

PhD / SYNOPSIS OF THIS THESIS The aim of this thesis is to more fully understand and explain the binding mechanism of organic molecules to the Au(111) surface and to explore the conduction of such molecules. It consists of five discreet chapters connected to each other by the central theme of “The Single Molecule Device: Conductance and Binding”. There is a deliberate concentration on azine linkers, in particular those with a 1,10-phenanthroline-type bidentate configuration at each end. This linker unit is called a “molecular alligator clip” and is investigated as an alternative to the thiol linker unit more commonly used. Chapter 1 places the work in the broad context of Molecular Electronics and establishes the need for this research. In Chapter 2 the multiple break-junction technique (using a Scanning Tunnelling Microscope or similar device) was used to investigate the conductance of various molecules with azine linkers. A major finding of those experiments is that solvent interactions are a key factor in the conductance signal of particular molecules. Some solvents interfere with the molecule’s interaction with and attachment to the gold electrodes. One indicator of the degree of this interference is the extent of the enhancement or otherwise of the gold quantized conduction peak at 1.0 G0. Below 1.0 G0 a broad range for which the molecule enhances conduction indicates that solvent interactions contribute to a variety of structures which could bridge the electrodes, each with their own specific conductance value. The use of histograms with a Log10 scale for conductance proved useful for observing broad range features. vi Another factor which affects the conductance signal is the geometric alignment of the molecule (or the molecule-solvent structure) to the gold electrode, and the molecular alignment is explored in Chapters 3 for 1,10-phenanthroline (PHEN) and Chapter 4 for thiols. In Chapter 3 STM images, electrochemistry, and Density Functional Theory (DFT) are used to determine 1,10-phenanthroline (PHEN) structures on the Au(111) surface. It is established that PHEN binds in two modes, a physisorbed state and a chemisorbed state. The chemisorbed state is more stable and involves the extraction of gold from the bulk to form adatom-PHEN entities which are highly mobile on the gold surface. Surface pitting is viewed as evidential of the formation of the adatom-molecule entities. DFT calculations in this chapter were performed by Ante Bilic and Jeffery Reimers. The conclusions to Chapter 3 implicate the adatom as a binding mode of thiols to gold and this is explored in Chapter 4 by a timely review of nascent research in the field. The adatom motif is identified as the major binding structure for thiol terminated molecules to gold, using the explanation of surface pitting in Chapter 3 as major evidence and substantiated by emergent literature, both experimental and theoretical. Furthermore, the effect of this binding mode on conductance is explored and structures relevant to the break-junction experiment of Chapter 2 are identified and their conductance values compared. Finally, as a result of researching extensive reports of molecular conductance values, and having attempted the same, a simple method for predicting the conductance of single molecules is presented based upon the tunneling conductance formula.

Le développement récent de l’électronique exige la mise au point de composants de plus en plus efficaces, de plus en plus rapides et de plus en plus réduits en taille. Dès les années 1970, il a été montré que l'on pourrait utiliser la molécule comme composante électronique élémentaire. Dans ce domaine, le chimiste sait aujourd’hui créer des molécules douées de propriétés remarquables, comme par exemple les molécules-aimants et les chaines-aimants qui montrent une bistabilité magnétique à basse température (T < 10 K) liée à la relaxation lente de leur aimantation, leur conférant ainsi la capacité de conserver l’information. Dans ce contexte, l’idée d’organiser des molécules-aimants par des connecteurs moléculaires photocommutables permet à la fois d’ajouter une propriété magnétique supplémentaire au matériau, mais également de photo-contrôler la bistabilité magnétique de ces objets. Dans ces travaux de thèse, nous nous sommes intéressés à l’association de molécules-aimants avec deux types de liens : les complexes à transfert de charge Na2[Fe(CN)5NO] et à conversion de spin [Fe(LN5)(CN)2] et [Fe(LN3O2)(CN)2] (LN5 et LN3O2 étant des ligands pentadentes) dans le but de photo-contrôler les propriétés magnétiques. Les résultats obtenus dans la partie dédiée à l’organisation des complexes [MnIII(BS)]+ via le précurseur photo-actif nitroprussiate se sont révélés décevants du point de vue photomagnétisme. Toutefois, un des nouveaux composés 2D présente un comportement magnétique de type molécule-aimant. La stratégie de connecter les précurseurs de [MnIII(BS)]+par des complexes photomagnétiques [Fe(LN3O2)(CN)2] et [Fe(LN5)(CN)2] pour synthétiser de nouveaux systèmes photosensibles a porté ces fruits puisque neuf nouveaux systèmes ont été synthétisés. Permi les résultats les plus significatifs, nous avons obtenu un système unidimensionnel dans lequel les unité dimères [MnIII2(BS)2]2+ sont connectées par l’entité photomagnétique et qui présente un comportement de molécule-aimant. On retiendra aussi un autre système unidimentionnel qui présente un ordre antiferromagnétique et de la relaxation lente de l’aimantation. D’autre part, les études photomagnétiques ont clairement montré des comportements photoinduits pour les cinq composés qui contiennent les centres FeII à l’état bas spin. Pour conclure, le développement de notre stratégie est prometteur pour la création de nouveaux matériaux photomagnétiques dans les années à venir. / The exponential growth of technological demands for information storage capacity is at the origin of the nanosciences and the development of the molecular electronics. Since more than 40 years, the main objective in this field of research is mainly to store as fast as possible more information in a smaller volume. Nowadays, chemists know how to create molecules with remarkable properties, such as Single–Molecule Magnets (SMMs) and Single–Chain Magnets (SCMs), which show magnetic bistability at low temperature (T < 10 K) providing a memory effect. Therefore, the design of novel materials with original physical properties, based on molecular magnetic objects, became the focus of many researches around the world. Following this approach, the design of SMM linked by active bridges that can switch between two magnetic states under external stimuli (temperature, pressure, light...), should favor additional properties and allow an external control (by irradiation) of the magnetic properties of the final SMM-based materials. The goal of this thesis is to organize SMMs by assembling them with two types of linkers: electron-transfer building blocks (Na2[Fe(CN)5NO]) and spin-crossover complexes ([Fe(LN5)(CN)2] and [Fe(LN3O2)(CN)2]). Three new materials obtained from the organization of [MnIII(BS)]+ complexes with the [Fe(CN)5NO]2- building-block, showed no significant photoactivity unlike the Na2[Fe(CN)5NO] precursor. Nevertheless, one of these organized systems exhibits Single-Molecule Magnet behaviour. The employed strategy to link [MnIII(BS)]+ units with photomagnetic [Fe(LN5)(CN)2] and [Fe(LN3O2)(CN)2] spin-crossover complexes, leads to nine new interesting compounds. The most significant novelty from a structural point of view is the various topologies of compounds obtained from molecular complexes to one-dimensional architectures with different arrangements. All compounds exhibit interesting magnetic properties. For example, one of the unidimensional networks shows an antiferromagnetic order followed by a slow relaxation of the magnetization that has been observed for the first time in a canted system. On the other hand, magnetic investigations under light irradiation have revealed remarkable photoinduced properties in the case of five systems based on FeII units in their low spin state. In conclusion, the synthetic strategy used in this thesis has been experimentally validated and opens new perspectives for future photomagnetic SMM and SCM systems.

Au cours de ce travail, une série de plateformes constituées d'un espaceur central connecté à deux complexes de MnII à haut spin a été synthétisée. De nombreux ligands ont été étudiés et greffés sur un ensemble d'espaceurs de longueur variant entre 1,5 et 5,5 nm. La distance Mn-Mn a été mesurée avec succès par résonance paramagnétique électronique (RPE) impulsionnelle à haut champ en utilisant la méthode PELDOR (Pulsed Electron-Electron Double Resonance). L'emploi de complexes de MnII avec de faibles valeurs d'éclatement en champ nul (ECN) a permis d'améliorer la sensibilité de cette méthode. Pour les plateformes constituées d'un espaceur polyproline, un bon accord a été observé entre la distribution de la distance Mn-Mn obtenue par PELDOR et par dynamique moléculaire, mais des composantes plus courtes dans la distribution ont été détectées pour certains paramètres expérimentaux. Ces observations ont été rationalisées en tenant compte du terme pseudo-séculaire de l'Hamiltonien dipolaire, non négligeable pour les systèmes étudiés où les spins observés et détectés sont similaires. Lorsqu'un espaceur rigide est employé, l'interaction pseudo-séculaire est bien plus marquée, ce qui se traduit par une distribution de distances plus large que prévu par la dynamique moléculaire. L'étude de nouveaux centres paramagnétiques pour la méthode PELDOR comme les radicaux trityl persistants a également été entreprise. Le tenseur g de ces radicaux a été déterminé avec précision par RPE à haut champ en utilisant MnII comme référence. Des calculs de DFT (Density Functional Theory) ont été effectués pour comprendre la relation entre la structure et le spectre RPE de ces radicaux trityl. / In this work, the synthesis of a set of platforms that incorporate a central linker of varying length connected to two high-spin MnII complexes has been performed. Several ligands were screened and efficient synthetic methodologies were developed to graft them on various spacers covering the 1.5 – 5.5 nm range. The Mn-Mn distance has been successfully measured using high-field pulsed electron paramagnetic resonance (EPR) spectroscopy, more precisely pulsed electron-electron double resonance (PELDOR). We showed that the use of MnII complexes with low zero-field splitting (ZFS) parameters led to an improved sensitivity. For flexible polyproline-based platforms, distances and distribution profiles obtained with PELDOR were in good agreement with molecular dynamics (MD) estimations, but additional features in the distance distributions could be observed under specific conditions. These finding were rationalized by taking into account the pseudo-secular term of the dipolar Hamiltonian, which was found to be non-negligible for the studied platforms, where pumped and detected spins are very similar. When the linker was rigid, the influence of the pseudo-secular interaction was much more prominent, leading to distance profiles with a higher width than predicted by MD calculations. Other emergent spin labels for pulsed EPR-based distance measurements such as persistent substituted trityl radicals were studied and their g-tensor was accurately measured using high-field EPR with MnII as an internal reference. Density functional theory (DFT) calculations were performed to understand the relationship between the structure and the EPR properties of the studied trityl radicals.

Ce travail a consisté en la synthèse d’outils chimiques et au développement de leurs applications biologiques. Dans un premier temps, des sondes pour l’étude de la Topoisomérase IIA humaine ont été synthétisées. Ces sondes ont alors été testées sur lysat cellulaire pour la capture des protéines présentant une affinité pour ces médicaments. Dans un second temps, un nouveau lien clivable en conditions non dénaturantes pour des applications en protéomique chimique a été developpé. Ainsi, après optimisation de la structure, il a été intégré au sein d’une sonde d’affinité pour évaluer sa capacité de capture et libération de la PARP 1. Enfin, la réaction de click entre un azoture et un cyclooctyne a été appliquée à l’élimination d’une drogue circulante dans le sang.Après l’étude cinétique de la réaction, l’activité biologique et la pharmacocinétique des différents composés ont été évaluées pour optimiser la réaction de click in vivo. / The main goal of this work was to synthesize chemical tools and to developp their biological applications. In the first part, probes for the study of Topoisomerase II via chemical proteomic were synthesized. They were then used for pulldown experiments on cell lysats. In a second part, a new cleavable linker in non denaturing conditions was developped for chemical proteomic applications. After optimisation of the structure, it was incorporated in an affinity probe and tested for the pulldown of PARP 1. Finally, a click chemistry reaction, the SPAAC, was used to provok the elimination of a circulating drug. After the study of the kinetic of the reaction, the biological activity and the pharmacokinetic of the different compounds were evaluated to optimise the click reaction in vivo.