A espectroscopia de molécula única (SMS) é uma poderosa técnica para entender como a conformação da cadeia polimérica é modificada por superfícies e interfaces. No presente trabalho, a interação substrato-polímero foi modificada pela alteração da carga superficial do substrato pela modificação do caráter hidrofóbico-hidrófilico da superfície do substrato. A conformação planar / não planar assumida pelo poli (9,9 dioctilfluoreno) (PFO) foi utilizada para acessar os efeitos de substratos e inter-cadeias sobre a conformação do polímero. Usamos a combinação de diferentes tratamentos para alterar superfícies de quartzo inerte de super hidrofílico (ângulo de contato ∼ 0°) para hidrofóbico (ângulo de contato ∼ 80°) quase continuamente. As películas ultrafinas de polímero (<10 nm) e moléculas isoladas podem ser depositadas em diferentes superfícies do substrato por técnica de revestimento por centrifugação de forma controlada, que permitiu a investigação de processos foto físicos a um nível molecular único. Utilizou-se três técnicas espectroscópicas para caracterizar tais filmes ultrafinos, a saber: microscopia de fluorescência confocal equipada com imagens de fluorescência espectral, espectroscopia de absorção UV / Vis e espectroscopia de fotoluminescência dependente da temperatura. As propriedades de emissão e eficiência de filmes de PFO ultrafinos são fortemente afetadas pela presença da interface do substrato. No caso de uma única cadeia de PFO, a fase planar (energia mais baixa) é induzida pela forte interação superfície-polímero no caso da superfície hidrofílica carregada. Além disso, esta interação pode ser fortemente perturbada ou inteiramente destruída por interações entre cadeias. / Single molecule spectroscopy (SMS) is a powerful technique to understand how polymeric chain conformation is modified by surfaces and interfaces [1]. In the present work, substrate-polymer interaction was modified by changing substrate superficial charge by the modification of the hydrophobic-to-hydrophilic character of the substrate surface or by the deposition of charged self-assembling monolayers or polyelectrolytes as well. The planar/non-planar conformation assumed by poly (9,9 dioctylfluorene) (PFO) was used to access the effects of substrates and interchain interactions on the polymer conformation [2]. We used the combination of dif-ferent treatments to change inert quartz surfaces from superhydrophylic (contact angle ∼ 0°) to hydrophobic (contact angle ∼ 80°) almost continuously. Polymer ultrathin films (<10 nm) and isolated chains can be deposited on different substrate surface by spin-coating technique in a controlled way that allowed the investigation of photophysical processes at a single molecular level. We employed three spectroscopic techniques to characterize such ultrathin films, namely: confocal fluorescence microscopy equipped with spectral facilities, UV/Vis absorption spectroscopy and temperature dependent photoluminescence spectroscopy. The emission properties and efficiency of ultrathin PFO films are strongly affected by presence of the inert substrate interface. In the case of single PFO chain, the planar phase (lower energy) is induced by the strong surface-polymer interaction in the case of charged hydrophilic surface. Moreover, this interaction can be strongly perturbed or entirely disrupted by interchain interactions.

L’étude de la chimie des actinides est essentielle dans le cadre de la technologie nucléaire pour le développement de nouveaux combustibles, pour l’étude du retraitement des déchets nucléaires et la migration des actinides dans l’environnement mais aussi pour la compréhension fondamentale des interactions actinide/ligand et la formation de liaisons multiples. Les propriétés magnétiques des molécules polymétalliques d’actinides sont particulièrement intéressantes pour explorer la communication magnétique entre différents centres métalliques. De plus, ces molécules ont été identifiées comme particulièrement prometteuses pour la conception de molécules aimants. L’uranium a une grande réactivité redox notamment due à ses multiples degrés d’oxydation accessibles et forme aisément des assemblages polynucléaires. Néanmoins, très peu de synthèses contrôlées de complexes polymétalliques d’uranium et de neptunium ont été décrites dans la littérature. La première approche de ce travail repose sur la synthèse de clusters oxo/hydroxo d’uranium à partir de l’hydrolyse contrôlée d’uranium tétravalent en présence d’un ligand organique rencontré dans l’environnement. Cette étude a mené à une famille de clusters aux topologies originales, dont la taille varie en fonction des conditions réactionnelles employées. Cependant les clusters obtenus ne mènjavascript:nouvelleZone('abstract');_ajtAbstract('abstract');ent pas à des propriétés de molécules aimants. Dans le but de favoriser une plus grande interaction entre les métaux par le ligand pontant, l’interaction cation-cation a été utilisée pour la synthèse rationnelle d’assemblages d’uranyle(V). Par le passé, peu de complexes d’uranyle(V) ont été isolés à cause de son instabilité vis-à-vis de la dismutation ; cependant, l’optimisation du ligand organique et des conditions de synthèse ont finalement permis de stabiliser l’uranyle(V). Nous avons utilisé des complexes stables d’uranyle(V) comme brique de base pour former des molécules hétéronucléaires avec des métaux 3d et 4f. Un réglage fin des conditions de réactions a mené à une conception rationnelle d’assemblages discrets ou polymériques. L’étude des propriétés magnétiques de ces assemblages d’uranium a mis en valeur des propriétés de molécules ou chaînes aimants avec de hautes valeurs d’énergie de relaxation. L’uranyle(V) a également été utilisé comme modèle structural du neptunium qui est plus radioactif permettant d’isoler un complexe isostructural homométallique de neptunyle(V) grâce à des conditions réactionnelles similaires. Finalement, des ligands nitrures favorisant la formation de liaison multiples uranium-ligand, ont été utilisés pour construire de nouveaux complexes binucléaires d’ujavascript:nouvelleZone('abstract');_ajtAbstract('abstract');ranium supportés par des ligands silanols. De nouvelles molécules, sans précédent, contenant des nitrures comme ligand pontant associés à de l’uranium au degré d’oxydation +III ont été isolées et caractérisées. / The study of actinide chemistry is not only essential for the development of nuclear fuel, nuclear fuel reprocessing or environmental clean up, but also for the understanding of fundamental actinide/ligand interactions and multiple bounding. The magnetic properties of polynuclear actinide molecules are of significant interest to investigate the magnetic communication between the metallic centres. Furthermore, they are highly promising for the design of molecular magnets. Uranium undergoes redox reactions due to a wide range of available oxidation states and easily forms polynuclear assemblies. However, only a few controlled synthetic routes towards these polynuclear uranium assemblies are described in the literature. In this context, the first part of this work was dedicated to the synthesis of oxo/hydroxo uranium clusters from the controlled hydrolysis of tetravalent uranium in the presence of an environmentally relevant ligand. This led to the synthesis of clusters with novel topologies, for which size could be varied as a function of the reaction conditions employed. However, the obtained clusters do not behave as SMM. In order to gain a stronger interaction between metallic centres, the cation-cation interaction was used to rationally design polynuclear uranyl(V) complexes. The isolation of uranyl(V) complexes had been limited in the past by its disproportionation, however, a fine tuning of the organic ligand and reaction conditions finally allowed to stabilise uranyl(V). We used stable uranyl(V) units as building block to form heteronuclear complexes with 3d and 4f metals with polymeric or discrete structures. The study of the magnetic properties of the uranium polynuclear assemblies was carried out and revealed single molecule or chain magnet behaviours with high energy barriers. The uranyl(V) unit was also used as a structural model for the more radioactive neptunium element, allowing the isolation of an isostructural trinuclear neptunyl(V) assembly in similar reaction conditions. Finally, the use of a nitride ligand as a bridging unit, allowing the formation of uranium-ligand multiple bonds, was explored to build novel di-uranium complexes supported by siloxy ligands. Nitride molecules containing unprecedented uranium in the +III oxidation state were isolated and characterised.

To respond to rapidly-changing stresses in their environment, bacterial cells must be able to sense a variety of chemical cues and respond to them by activating the relevant genes. The lysine riboswitch is a short RNA motif, located just upstream of a gene encoding a lysine biosynthesis protein, that suppresses the expression of that gene when sufficient lysine is present in the cell. It acts by binding a lysine monomer in a region called the aptamer, which in turn rearranges an adjacent domain called the expression platform, sequestering the ‘start' sequence of the gene and preventing it from being transcribed. In this thesis, the lysine riboswitch's ligand-binding transition is studied using single-molecule fluorescence microscopy, optical tweezers, and a hybrid optical force/fluorescence technique. Förster Resonance Energy Transfer (FRET) is used with a fluorescently-labeled aptamer to show that it has a previously-undescribed, partially-folded structural state with enhanced ligand affinity compared to the unfolded structure. The Mg²⁺ dependence of the transition between these states is shown to resolve existing debates in the literature about the sensitivity of the riboswitch. The kinetics of the folding transition are explored using FRET, optical force, and hybrid ‘Fleezers' to map the free energy landscape of ligand binding and show that the ligand itself promotes transitions into the aptamer's folded state, a so-called ‘induced fit' mechanism rare among riboswitches. Finally, high-resolution optical tweezers are used to explore the link between the aptamer's secondary structure (the sequence of paired nucleotides) and its tertiary structure (three-dimensional folding) to illuminate the role of ligand binding in gene regulation, which depends on the equilibrium between competing secondary structures. Hybrid biophysical techniques like optical force/fluorescence microscopy are shown to be indispensable for addressing all the states in the reaction pathways of complex biomolecules like riboswitches and for discriminating between multiple levels of structure formation and interaction with the environment. Not only do the results presented here shed light on the RNA folding problem, particularly the role of tertiary structure in determining the minimum-energy configuration of an RNA sequence, but they could have implications for biomedical research, as the lysine riboswitch has already been shown to be a potential target for next-generation antibiotics.

No description available.

L'ARN s'est longtemps vu attribuer un simple role de transmission entre l'ADN, garant de l'information genetique, et les proteines, assurant les fonctions et donc la survie cellulaire. Ce n'est qu'avec les decouvertes des ARNs de transfert dans les annees 70, puis des ribozymes dans les annees 80, qu'il a ete realise que l'ARN pouvait assurer ces deux roles : l'information genetique est stockee dans sa sequence lineaire, et l'adoption de structures tridimensionnelles complexes rend possible une activite catalytique. Depuis, de nouvelles fonctions de l'ARN n'ont cesse d'etre decouvertes, a tous les niveaux de regulation de l'expression genique entre autres. La majorite de ces fonctions repose sur la structuration tridimensionnelle d'ARNs simple brin.Dans ce travail, differents aspects de la structuration de l'ARN sont abordes, toujours en utilisant la technique de mesure de forces sur molecules uniques par piegeage optique. Dans un premier temps, une etude comparative d'une structure secondaire modele, le hairpin dans ses formes ARN et ADN, a ete realisee. La question de l'interaction d'une structure secondaire avec une proteine helicase (DbpA) a ensuite ete abordee. Enfin, dans le cadre plus general d'une etude sur l'assemblage du ribosome, nous avons debute le developpement d'une nouvelle methode d'analyse des structures secondaires. Cette methode repose sur le suretirement d'un hybride ARN ribosomique / ADN. / Traditionally, RNA has been considered as a mere intermediate between DNA, keeper of the genetic information, and proteins, which assume cells self-sustenance. With the discoveries of the transfert RNA in the 70s, and of the ribozymes in the 80s, RNA took on both roles: it can store information in its linear sequence, and tridimensional structuration enables catalytic functions. Since then, numerous roles devoted to RNA have been discovered, particularly for gene expression regulation. Most of these functions rely on tridimensional structuration of single stranded RNA. In this work, we used an optical tweezers setup to study several aspects of RNA structuration by single molecule force measurement. In a first part, we compared the dynamic behaviour of a model secondary structure made of either RNA or DNA, the hairpin. Then we considered the interaction of a secondary structure with a protein, the RNA helicase DbpA. Finally, within a wider study of ribosome assembly, we worked on the development of a new method to study tridimensional structuration. This method relies on the overstretching of a hybrid ribosomal RNA / DNA molecule.

La protéine SRSF1, aussi appelée ASF/SF2, fait partie de la famille des protéines SR, une famille de protéines liant l’ARN très conservées. Ces protéines jouent un rôle régulateur de l’épissage, également lors de l’épissage alternatif. Une centaine d’ARN cible ont été décrits pour SRSF1 mais la manière dont SRSF1 sélectionne ses cibles parmi tous les pré-ARNm est mal comprise. Des études in vitro et in vivo ont montré que les protéines SR reconnaissent un petit motif dégénéré qui est souvent présent en plusieurs copies dans les ESE («enhancer splicing element »). Bien que les protéines SR lient ces motifs avec une faible spécificité, la définition des exons se fait avec une grande fidélité. Afin de mieux comprendre le mécanisme d’action de SRSF1, j’ai réalisé une étude cinétique des interactions SRSF1-ARN dans les cellules vivantes par des techniques de microscopies avancées. Grâce au système CRISPR, j’ai pu étiqueter la protéine SRSF1 avec la protéine Halo puis j’ai combiné une technique de photo-blanchiment (FRAP) et une technique de suivi de particule unique (« single particle tracking, SPT) pour mesurer la diffusion de SRSF1 et son affinité pour l’ARN. J’ai mesuré la durée de vie des événements de liaison individuellement aussi bien sur le pool global de pré-ARNm que sur des cibles spécifiques. Nos résultats indiquent que la liaison de SRSF1 ne dépasse pas quelques secondes, même sur les cibles de haute affinité. Cette cinétique rapide permet à SRSF1 d’être en contact avec l’ensemble des transcrits naissants qui est produit en permanence dans la cellule. De plus, mon travail apporte une analyse cinétique de la dynamique des snRNP à la résolution de la molécule unique dans le nucléoplasme des cellules vivantes. Nous avons déterminé les coefficients de diffusion des snRNP et la durée de leur association à l’ARN dans ces cellules. / SRSF1, formerly known as ASF/SF2, belongs to the SR protein family, which is a conserved family of RNA-binding protein that plays essential roles as regulators of both constitutive and alternative splicing. Hundreds of RNA targets have been described for SRSF1 but how SRSF1 selects its targets from the entire pool of cellular pre-mRNAs remains an open question. In vitro and in vivo studies have shown that SR proteins recognize short degenerated motifs often present in multiple copies at ESEs. Similar cryptic motifs are however frequently present in pre-mRNAs, and this low specificity of binding contrasts with the great fidelity of exon definition. To better understand the mechanism of action of SRSF1, I performed a kinetic study of SRSF1-RNA interactions in live cells using advanced microscopic techniques. Taking advantage by the CRISPR system, I tagged endogenous SRSF1 with Halo protein, and I combined photobleaching (FRAP) and single particle tracking (SPT) techniques to estimate diffusion and binding rates of SRSF1. I measured the duration of individual binding events, both on the cellular pool of pre-mRNAs and on specific targets. Our results indicate that binding of SRSF1 does not exceed few seconds, even on high-affinity targets. This rapid kinetics allows SRSF1 to rapidly sample the entire pool of nascent RNAs continuously produced in cells. Moreover, we provided a kinetic analysis of snRNP dynamics at a single-molecule resolution in the nucleoplasm of living cells. Our results enabled us to determine diffusion coefficients of snRNPs and their RNA binding duration in vivo.

Disruptions in the response of endothelial progenitor cells to changes in oxygen environment may present a possible mechanism behind multiple pediatric pulmonary disease models, such as bronchopulmonary dysplasia. Using high-throughput fixed single-cell protein and RNA imaging, we have created "stop-motion" movies of Thymosin. 4 (T beta 4) and Hypoxia Inducible Factor 1 alpha (HIF-1 alpha) protein expression and vascular endothelial growth factor (vegf) and endothelial nitric oxide synthase (eNOS) mRNA in human umbilical cord-derived endothelial colony-forming cells (ECFC). ECFC were grown in vitro under both room air and hyperoxia (50% O-2). We find elevated basal T beta 4 protein expression in ECFC derived from prematurely born infants versus full term infants. T beta 4 is a potent growth hormone that additionally acts as an actin sequestration protein and regulates the stability of HIF-1 alpha. This basal level increase of T beta 4 is associated with lower HIF1 alpha nuclear localization in preterm versus term ECFC upon exposure to hyperoxia. We find altered expression in the pro-angiogenic genes vegf and eNOS, two genes that HIF-1 alpha acts as a transcription factor for. This provides a potential link between a developmentally regulated protein and previously observed impaired function of preterm ECFC in response to hyperoxia.

No description available.

Over the past decade, solid-state nanopores have emerged as a versatile tool for the detection and characterization of single molecules, showing great promise in the field of personalized medicine as diagnostic and genotyping platforms. While solid-state nanopores offer increased durability and functionality over a wider range of experimental conditions compared to their biological counterparts, reliable fabrication of low-noise solid-state nanopores remains a challenge. In this thesis, a methodology for treating nanopores using high electric fields in an automated fashion by applying short (0.1-2 s) pulses of 6-10 V is presented which drastically improves the yield of nanopores that can be used for molecular recognition studies. In particular, this technique allows for sub-nanometer control over nanopore size under experimental conditions, facilitates complete wetting of nanopores, reduces noise by up to three orders of magnitude and rejuvenates used pores for further experimentation. This improvement in fabrication yield (over 90%) ultimately makes nanopore-based sensing more efficient, cost-effective and accessible. Tuning size using high electric fields facilitates nanopore fabrication and improves functionality for single-molecule experiments. Here, the use of nanopores for the detection of DNA-protein complexes is examined. As proof-of-concept, neutravidin bound to double-stranded DNA is used as a model complex. The creation of the DNA-neutravidin complex using polymerase chain reaction with biotinylated primers and subsequent purification and multiplex creation is discussed. Finally, an outlook for extending this scheme for the identification of proteins in a sample based on translocation signatures is presented which could be implemented in a portable lab-on-a-chip device for the rapid detection of disease biomarkers.

In order for molecular magnetic materials to become applicable, they must retain their magnetisation at reasonable temperatures, which can be achieved with high energy barriers for spin reversal and high blocking temperatures. In the field of Single-Molecule Magnets (SMMs), over the last decade, the main focus has shifted from large spin complexes to highly anisotropic systems which have displayed record energy barriers. There are two main methods of increasing magnetic anisotropy in a complex: i) Choosing a metal ion that boasts high magnetic anisotropy then coupling two such ions through magnetic interactions to induce large global anisotropy, and ii) maintain a low spin or use a mononuclear complex while minimising quantum tunnelling of the magnetisation by controlling the geometric features of the metal ion. Both strategies are equally valid and have been explored in this thesis using dinuclear lanthanide as well as mononuclear 3d complexes. In the pursuit of high-barrier SMMs via alignment of anisotropy axes, two dinuclear, quadruple-stranded helicates and one mesocate were isolated and are described in detail herein, both structurally and magnetically. Furthermore, theoretical calculations have been performed to determine the energies of Kramers doublets on each DyIII centre to derive magneto-structural correlations. To induce magnetic interactions between DyIII ions, a centrosymmetric dinuclear SMM was synthesised. Investigation of the crucial DyIII…DyIII interaction as well as its effect on the quantum tunnelling of the magnetisation has been carried out using ab initio calculations and magnetic dilution studies. Using the same system, a method of greatly enhancing the energy barriers in SMMs has been developed. It involves modifying the coordinating ligands to include electron withdrawing groups in order to yield more anisotropic metal ions. The energy barrier for spin reversal has been increased 7-fold in one case. While lanthanide chemistry has proven to be quite versatile and promising, a new branch of nanomagnets is currently being pursued: mononuclear 3d complexes as SMMs. The advantages of 3d metals include high anisotropy per ion, low spin (as anisotropy decreases with increasing spin), well-understood electronic structures and clear correlations between geometry and magnetic anisotropy. The structural and magnetic properties of three complexes based on CoII and terpyridine ligands as well as a seven-coordinate CoII complex with positive anisotropy are discussed at length. The unique slow relaxation dynamics and spin crossover behaviour has been followed using DFT and ab initio calculations, as well as EPR and magnetic dilution studies. Overall, this thesis describes the efforts taken to synthesise high-barrier nanomagnets through understanding the origins and mechanisms of slow magnetic relaxation in both lanthanide and 3d metal complexes.