Le rayonnement UV solaire induit des modifications de la structure chimique des bases nucléiques de l'ADN essentiellement au niveau de site dipyrimidinique et conduit principalement à la formation des adduits cyclobutanique et (6-4). Ces adduits sont impliqués dans le photovieillisement et le cancer cutané. Les adduits (6-4) sont potentiellement les plus dangereux en raison de leurs propriétés mutagènes intrinsèques.La conformation de l'ADN représente l'un des facteurs gouvernant la formation de l'adduit (6-4). Afin, d'identifier les paramètres structuraux favorisant sa formation, des analogues du dinucléotide de thymine, de conformation choisie, ont été synthétisés. Les modifications chimiques apportées au sein des dinucléotodes ont permis de déplacer l'équilibre conformationnel Nord/Sud du désoxyribose de la thymidine, vers une conformation majoritaire souhaitée. Une analyse structurale par dichroïsme circulaire et une étude préliminaire de photoréactivité ont été réalisées sur ces dinucléotides modifiés. Les résultats obtenus révèlent l'implication de formes minoritaires empilées de ces dinucléotides dans la formation de l'adduit (6-4). De plus, l'étude photochimique montre que l'augmentation de conformères Nord et Sud du dinucléotide aux extrémités 5' et 3', respectivement, favorise la formation de l'adduit (6-4). Cependant, une conformation totalement contrainte Nord et Sud aux extrémités 5' et 3', respectivement, défavorise sa formation.Ces résultats ont permis d'identifier une conformation augmentant le rendement de formation de l'adduit (6-4) et permettront de concevoir de nouveaux modèles conduisant à la formation exclusive de ces adduits. Ces modèles pourront être utilisés en biologie en vue d'applications thérapeutiques ou comme outil en biophysique afin d'élucider le mécanisme de formation de cet adduit. / Exposure of DNA to solar UV light induces chemical modifications on its nucleic bases that are responsible for photoaging and skin cancer. Two major DNA photoproducts class exist: cyclobutane and (6-4) adducts. The latter is intrinsically more mutagenic than the cyclobutane adduct and therefore potentially more dangerous.DNA conformational parameters influence (6-4) adducts formation. To identify structural factors governing (6-4) adduct formation; we synthesized dinucleotides endowed with a specific conformation. Nucleoside moieties exist in a dynamic equilibrium between North and South conformation. Nucleoside conformational changes have been introduced by chemical modifications to obtain desired conformations. Then a structural study by circular dichroism correlated with photochemical study was done. It showed that minor stacked conformers promote (6-4) adduct formation. Moreover, the photochemical study reveals that the increase of North and South conformers at the 5' and 3' end, respectively, increased (6-4) adduct formation but a locked dinucleotide almost precluded (6-4) adduct formation. This result helps to design new models favoring (6-4) adduct formation. Understanding the conformational parameters that govern (6-4) adduct formation will facilitate the development of new therapeutic strategies and the elucidation of the (6-4) adducts formation mechanism.

Tritrpticina (TRP3) é um peptídeo antimicrobiano com 13 resíduos de amino ácidos com três Ws sequenciais. Com o objetivo de contribuir para a compreensão de seu mecanismo de ação, realizaram-se estudos funcionais e conformacionais da TRP3 e de dois análogos onde um (WLW) ou dois (LWL) W foram substituídos por L. Os peptídeos foram igualmente ativos contra bactérias Gram positivas e negativas. Sua atividade hemolítica requereu concentrações maiores, diminuindo na ordem TRP3>WLW>LWL. Os peptídeos permeabilizaram membranas modelo de E. coli ou contendo fosfolipídios carregados negativamente. Espectros de CD sugeriram que os peptídeos adquirem diferentes conformações ao se ligarem a bicamadas e micelas. Estudos de fluorescência mostraram que a ligação a membranas decresce na ordem: TRP3>WLW>LWL e que os peptídeos se localizam próximos à interface membrana-água. Espectros de RPE de marcadores de spin lipídicos indicaram que a ligação dos peptídeos altera a organização dos lipídios, aumentando o empacotamento molecular / Tritrpticin (TRP3) is a 13-residue antimicrobial peptide that contains three sequential Ws. With the aim of contributing to the understanding of its mechanism of action, functional and conformational studies were performed with TRP3 and two of its analogues where one (WLW) or two (LWL) of the W were replaced by L. The peptides were equally active against both Gram positive and Gram negative bacteria. Higher concentrations were required for hemolytic activity which varied in the order: TRP3>WLW>LWL. The peptides permeabilized membranes model membranes mimicking E. coli\'s lipid composition or containing different negatively charged phospholipids. CD spectra suggested the peptides acquired different conformations upon binding to bilayers or micelles. Fluorescence studies showed that membrane binding decreases in the order: TRP3>WLW>LWL and that the peptides are located close to the water-membrane interface. EPR spectra of lipid spin labels indicated that peptide binding alter lipid organization, increasing molecular packing

Dynamical effects are known to reduce the signal to noise ratio in EMCD measurements making them highly dependent on sample thickness. Precession of the electron beam has been shown to reduce these effects in ordinary crystallography. This work investigates precession of the electron beam as a method of reducing the dynamical effects in EMCD using simulations. Simulations are run on BCC Fe in two and three beam conditions. The results show significant effects on the EMCD signal. However, whether these improve the signal quality seems dependent on sample orientation and thickness range. The initial findings reported here are promising and motivate further research.

Dans le but de rechercher de nouveaux inhibiteurs de l’ARN polymérase NS5 du virus de la dengue (DENV), un criblage a été mené sur 650 plantes néo-calédoniennes. A la suite de ce criblage, deux espèces (Cryptocarya chartacea Kostermans et Trigonostemon cherrieri Veillon) ont été sélectionnées. L’extrait AcOEt des écorces de Cryptocarya chartacea (Lauraceae) a montré une forte inhibition de la NS5 polymérase (99 % à 10 µg/ml). L’étude phytochimique de l’extrait a mis en évidence une série de nouvelles flavanones 6-mono et 6,8-dialkylées, nommées chartacéones. Celles-ci sont présentes sous forme de mélanges racémiques au sein de C. chartacea. La chartacéone A a été purifiée sur colonne chirale conduisant à l’isolement de quatre diastéréoisomères optiquement purs. Une étude configurationnelle basée sur le calcul théorique de spectres de dichroïsme circulaire a permis la détermination de leur configuration absolue. Les chartacéones inhibent de façon sélective la NS5 polymérase du DENV. L’étude des extraits AcOEt des écorces et du bois de Trigonostemon cherrieri (Euphorbiaceae) a mis en évidence une série de métabolites secondaires originaux de type Diterpènes Daphnane Orthoester (DDO) chlorés : les trigocherrines (non-macrocycliques) et les trigocherriolides (macrocycliques). Ces composés ont montré une inhibition de l’activité enzymatique de la NS5 polymérase du DENV et une activité antivirale sur le virus du chikungunya in cellulo. / In order to identify new inhibitors of the dengue virus (DENV) NS5 RNA polymerase, a screening was led on 650 new-caledonian plants. Two species, Cryptocarya chartacea Kostermans and Trigonostemon cherrieri Veillon were selected. The EtOAc bark extract of Cryptocarya chartacea (Lauraceae) showed a potent inhibition of the NS5 polymerase activity (99 % at 10 µg/ml). The phytochemical study of the extract led to the isolation of a series of new 6-mono and 6,8-dialkylated flavanones, called chartaceones. Chartaceones are present as racemic mixtures in the plant. Chartaceone A was purified on chiral column leading to the isolation of 4 optically pure diastereoisomers. A configurational study based on the theoretical calculation of circular dichroism spectra allowed the determination of their absolute configuration. Chartaceone are selective inhibitors of the DENV NS5 polymerase. The study of the EtOAc extract from the bark and wood of Trigonostemon cherrieri (Euphorbiaceae) led to the isolation of a series of unusual chlorinated daphnane diterpene orthoesters (DDO) : trigocherrins (non macrocylic) and trigocherriolides (macrocyclic). These compounds inhibit the DENV NS5 polymerase activity and present an antiviral activity on the chikungunya virus in cellulo.

Ce travail est consacré à l’étude des effets de chiralité dans des dipeptides cycliques construits sur un cycle dikétopiperazine (DKP) et comportant deux résidus de chiralités identiques ou opposées, LL et LD. Les mêmes systèmes sont étudiés dans différents environnements par spectroscopie optique couplée à des calculs de chimie quantique. Les molécules neutres sont isolées et refroidies en jet supersonique et caractérisées par spectroscopie laser UV et IR sélective en conformère. La structure des systèmes protonés, isolés dans un spectromètre de masse ICR, est déterminée par spectroscopie de dissociation induite par absorption de multiples photons IR. Enfin, le dichroïsme circulaire vibrationnel (VCD) est appliqué aux échantillons en phase solide. Les systèmes étudiés comportent un résidu aromatique tyrosine (cyclo Tyr-Pro) ou phénylalanine (cyclo Phe-Phe et Phe-His). Le diastéréomère LD est en général moins stable et plus flexible que LL, et ils ne diffèrent structurellement que par des interactions faibles de type NH…π ou CH…π. Le conformère le plus stable correspond en général à une structure où le chromophore aromatique est replié sur le cycle peptidique, l’autre partie étant étendue. Un effet très important de la chiralité est observé dans certains dimères protonés. Enfin, les expériences de VCD en phase condensée montrent que la phase cristalline de cyclo LPhe-DPhe formée par déshydratation du dipeptide linéaire en phase solide est chirale à cause de la synchronisation des chiralités transitoires des monomères. / This work focuses on the study of chirality effects on the structure of cyclic dipeptides built on a diketopiperazine (DKP) ring with residues of identical (LL) or opposite (LD) chirality. The same systems are studied in different environments by means of optical spectroscopy coupled to quantum chemical calculations. The neutral molecules are isolated and cooled down to a few K in a supersonic expansion and characterized by UV and conformer-specific IR laser spectroscopy. The structure of the protonated systems, isolated in an ICR mass spectrometer, is determined by infrared multiple photon dissociation spectroscopy. Last, vibrational circular dichroism (VCD) is applied to the solid-state samples.The studied systems possess an aromatic residue, either tyrosine (cyclo Tyr-Pro) or phenylalanine (cyclo Phe-Phe and Phe-His). The LD diastereomer is in most of the cases less stable and more flexible than LL. LL and LD differ from each other by weak interactions like NH…π or CH…π interactions. The most stable conformer usually corresponds to a structure with the aromatic chromophore folded over the DKP ring, the other part being extended. A dramatic effect of chirality is observed for some of the protonated dimers. Last, VCD experiments in the condensed phase show that the crystal phase of LPhe-DPhe formed by solid-state dehydration of the linear dipeptide is chiral due to synchronization of the transient chirality of the monomers.

The thesis aims at the study of conformation of a dimethyl tartrate molecule using the methods of vibrational optical activity (VOA), namely vibrational circular dichroism (VCD) and Raman optical activity (ROA). Based on the theoretical background of both VOA methods and current state of research of the studied molecule there was a sample of dimethyl tartrate dissolved in different solvents and its properties were measured using VCD and ROA spectrometers. In addition to the experiment, ab initio calculations were carried out in order to compare calculated and experimental spectra. Based on the comparison, the possible conformations present in water solution of the studied molecule are described in detail.

Lactobacillus kunkeei is the most common and dominant bacterium in the honey stomach of honeybees. L. kunkeei has been isolated from honeybees all over the world. Genome sequencing has identified 5 genes for exceptionally large proteins in the genome of L. kunkeei. These proteins do not show any similarity to sequences of proteins with a known structure. These giant proteins all have a conserved region of 60 amino acids in their C-terminus. This conservation led to the hypothesis that the C-terminal domains of the giant proteins are important for their function with possibly a role in the attachment to the cell wall. In this study, a total of eight different constructs were made for two of these giant proteins. The boundaries for the constructs were determined based on bioinformatic predictions. The eight constructs all have different start positions and all end at the very C-terminal end of the protein. These constructs were cloned into an expression vector. One of the full-length giant protein was cloned into an expression vector as well.  The C-terminal constructs and the full-length proteins were recombinantly produced in Escherichia coli. Expression of six C-terminal constructs was observed and an attempt was made to purify two of the C-terminal constructs. Expression of the full-length giant protein was observed as well and purification was attempted. Neither the C-terminal constructs nor the full-length giant protein could be purified at full length. The results for the C-terminal constructs show that no folded C-terminal domain has been found for the giant proteins. A purified protein construct of the N-terminal of one of the giant proteins was available. This protein was analyzed using biophysical techniques. Circular dichroism was used to test the thermal stability. The construct did not refold after being thermally denatured. Circular dichroism measurements indicated that the N-terminal construct is composed of a mixture of α-helices and ß-sheets. Small-angle X-ray scattering data indicated that the N-terminal construct had an elongated shape with knot-like parts. Protein crystals have been obtained for the N-terminal construct and these will be analyzed using X-ray diffraction.

Atoms change their optical properties drastically when combined into molecules or crystals. This becomes evident when comparing isolated carbon atoms with their solid-state polymorphs graphite and diamond. Plasmonic meta-surfaces adopt this concept to design the optical properties of thin films at will. In analogy to natural materials, the optical response of a meta-surface is dictated by the arrangement and plasmonic coupling (hybridization) of sub-wavelength metallic objects, so-called meta-atoms, rather than by the individual components. Although traditional direct writing approaches offer a high degree of freedom in design of nanostructures, reconfiguration of meta-atoms is usually limited. Especially their spatial rearrangement remains a huge challenge. Postfabrication tunability, however, would be crucial to advance device miniaturization and optical computing, by introducing dynamically tunable optics and optical switches. This thesis investigates colloidal assembly as a cost-efficient approach to fabricate meta-surfaces on cm²-areas whose optical properties can be tuned by geometrical reconfiguration. Hydrodynamic fields and topographical templates guide the deposition of colloidal nanoparticles with precise orientational and/or positional control. In the course of this work, the level of particle assembly complexity is successively increased to realize 1-, 2-, and 3-dimensional (1D, 2D, 3D) plasmonic assemblies. Strongly correlated with assembly geometry, different aspects of light are controllable. (I) 1D alignment of silver nanowires (AgNWs) produces differential transmission for linear polarization states (linear dichroism). (II) Single particles in a 2D square array interact coherently to produce a sharp, so-called surface lattice resonance (SLR). This effect confines strong electromagnetic fields in the lattice plane, which is promising for plasmonic lasing. (III) 3D chiral, cross-stacked particle chains control the transmission of circular polarization states (circular dichroism, CD). The unique advantages of colloidal assembly are demonstrated. (I) Spray coating allows rapid deposition of oriented AgNWs over large areas and is compatible with roll-to-roll processing. Employing wrinkle-structured receiver substrates, gradients of continuously varying linear dichroism are feasible in a single step. (II) Capillary assembly is able to realize ~1 nm inter-particle spacing, which is not achievable by conventional top-down lithographical methods. The small spacing enhances inter-particle plasmon coupling and boosts CD in cross-stacked, chiral particle chains, as presented in this thesis. (III) Such hierarchical and restackable, chiral structures make large volumes of superchiral fields accessible for ultrasensitive, enantioselective detection of analytes. This is in vast contrast to stacked nanobars produced via lithography where the most pronounced fields in the inter-layer gap are blocked by the presence of spacing layers. A central focus of this thesis is the postfabrication reconfiguration of the systems presented. This in-situ tunability is realized by elastic and reversibly stackable templates. (I) Uniaxial, mechanical strain converts the 2D square lattice into a rectangular one. This splits the SLR into two polarization-dependent modes whose resonance position is shifted reversibly when load is applied. (II) The cross-stacked, chiral particle chains are restackable. This allows adjustment of the stacking angle to tune CD magnitude and sign. (III) Reversible compression of this chiral stack induces a bending of the chains to shift the spectral position of CD modes. In a proof of concept, locally varying compression is shown to create a gradient of CD response as important step towards on-chip CD spectroscopy. Overall, this thesis (I) tests the limits of colloidal assembly by going from single-particle arrays to complex 3D arrangements; (II) explores geometrical reconfiguration of these plasmonic nanostructures to tune pronounced optical effects. The strategies presented herein can be extended to other colloidal particle shapes and materials. Moreover, the concepts of restackable meta-surfaces and local compression for tuning optical response open an intriguing playground and might inspire top-down approaches as well. / Atome ändern ihre optischen Eigenschaften drastisch, wenn sie sich zu Molekülen oder Kristallen vereinigen. Dies wird deutlich, wenn man isolierte Kohlenstoffatome mit ihren Festkörperpolymorphen Graphit und Diamant vergleicht. Plasmonische Meta-Oberflächen übernehmen dieses Konzept, um die optischen Eigenschaften dünner Schichten nach Belieben einzustellen. In Analogie zu natürlichen Materialien wird die optische Antwort einer Meta-Oberfläche durch die Anordnung und plasmonische Kopplung (Hybridisierung) metallischer Mikro- und Nano-Objekte, den sogenannten Meta-Atomen, bestimmt und kann sich stark von den Eigenschaften der Einzelkomponenten unterscheiden. Obwohl traditionelle Direktschreibverfahren ein hohes Maß an Gestaltungsfreiheit in der Nanostrukturierung bieten, ist die Rekonfiguration von Meta-Atomen in der Regel begrenzt. Vor allem ihre räumliche Neuordnung bleibt eine große Herausforderung. Eine Durchstimmbarkeit auch nach der Herstellung zu gewährleisten wäre jedoch entscheidend, um die Miniaturisierung von Geräten und die Realisierung optischer Computer—durch die Einführung dynamisch durchstimmbarer optischer Bauteile und optischer Schalter—voranzutreiben. Diese Dissertation untersucht kolloidale Assemblierung als kostengünstigen Ansatz zur Herstellung von Meta-Oberflächen im cm²-Maßstab, deren optische Eigenschaften durch geometrische Rekonfiguration durchgestimmt werden können. Hydrodynamische Felder und topographische Template steuern die Ablagerung kolloidaler Nanopartikel mit präziser Orientierungs- und/oder Positionskontrolle. Im Verlauf dieser Arbeit wird die Komplexität der Partikelanordnung sukzessive erhöht, um 1-, 2- und 3-dimensionale (1D, 2D, 3D), plasmonische Anordnungen zu realisieren. Eng verbunden mit der Anordnungsgeometrie können verschiedene Aspekte des Lichts gesteuert werden. (I) Die 1D-Ausrichtung von Silbernanodrähten ruft unterschiedliche Transmission für lineare Polarisationszustände hervor (linearer Dichroismus). (II) Einzelpartikel in einem quadratischen 2D-Kristall wechselwirken kohärent, was eine scharfe, sogenannte Oberflächengitterresonanz (surface lattice resonance) erzeugt. Dieser Effekt konzentriert starke elektromagnetische Felder in der Gitterebene, was ihn für plasmonische Laser interessant macht. (III) 3D-chirale, über Kreuz geschichtete Partikelketten beeinflussen die Transmission zirkularer Polarisationszustände (zirkularer Dichroismus). Die einzigartigen Vorzüge der kolloidalen Assemblierung werden aufgezeigt. (I) Die Sprühbeschichtung ermöglicht eine rasche Abscheidung orientierter Silbernanodrähte auf großen Flächen und lässt sich mit kontinuierlicher Fertigung (Rolle-zu-Rolle) verbinden. Mit Hilfe faltenstrukturierter Substrate können Gradienten mit kontinuierlich variierendem Lineardichroismus in einem einzigen Schritt erzeugt werden. (II) Partikelanordnung mittels Kapillarkräften ermöglicht Partikelabstände von ~1 nm, was mit herkömmlichen, lithographischen Methoden nicht erreichbar ist. Dieser geringe Abstand verbessert die Plasmonenkopplung zwischen den Partikeln und verstärkt den Zirkulardichroismus in gekreuzten, chiralen Partikelketten, wie in dieser Arbeit vorgestellt wird. (III) Solche hierarchischen und wiederholt stapelbaren, chiralen Strukturen machen große Volumina an superchiralen Feldern für Analytmoleküle zugänglich, was deren ultrasensitive, enantioselektive Detektion ermöglicht. Dies steht in starkem Gegensatz zu gestapelten, lithographisch hergestellten Nanostäbchen, bei denen die stärksten Felder im Zwischenschichtspalt durch die Anwesenheit von Abstandsschichten versperrt bleiben. Ein zentrales Thema dieser Arbeit ist die Rekonfiguration der vorgestellten Systeme im Anschluss an deren Fertigung. Diese in-situ-Durchstimmbarkeit wird durch elastische und reversibel stapelbare Template realisiert. (I) Mechanische Deformation entlang einer Achse überführt den quadratischen 2D-Kristall in einen rechteckigen. Dadurch wird die Oberflächengitterresonanz in zwei polarisationsabhängige Moden aufgespalten, deren Resonanzposition unter Krafteinwirkung reversibel verschoben wird. (II) Die über Kreuz gestapelten, chiralen Partikelketten sind wiederholt stapelbar. Dies ermöglicht die Anpassung des Stapelwinkels, um die Stärke und das Vorzeichen des Zirkulardichroismus einzustellen. (III) Reversible Kompression dieses chiralen Stapels verursacht ein Verbiegen der Ketten und verschiebt so die spektrale Position der zirkulardichroitischen Moden. In einer Machbarkeitsstudie konnte gezeigt werden, dass lokal variierende Kompression einen Gradienten des Zirkulardichroismus hervorruft. Dies stellt einen wichtigen Schritt in Richtung Ein-Chip-Spektroskopie dar. Diese Arbeit (I) lotet die Grenzen der kolloidalen Assemblierung aus, indem sie von Einzelpartikel-Anordnungen zu komplexen 3D-Arrangements übergeht; (II) untersucht die geometrische Rekonfiguration dieser plasmonischen Nanostrukturen, um ausgeprägte optische Effekte zu modulieren. Die hier vorgestellten Strategien können auf andere kolloidale Partikelformen und materialien übertragen werden. Darüber hinaus bereiten die Konzepte wiederholt stapelbarer Meta-Oberflächen und der lokalen Kompression zum Einstellen der optischen Eigenschaften eine faszinierende Spielwiese. Auch der Top-Down-Fertigung könnten diese Ansätze als Blaupause dienen.

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