Due to a lack of fundamental knowledge about the role of molecular structures in molecular electronic devices, this research is focused on the development of instruments to understand the relation between device design and the electronic properties of electroactive components. The overall goal is to apply this insight to obtain a more efficient and reliable scheme and greater functional control over each component. This work developed a fabrication method for porphyrinoids on graphene-based field effect transistors (FETs), and a chemical sensing platform under an ambient environment by integrating a tip-enhanced Raman spectroscope (TERS), atomic force microscope (AFM), and electronic testing circuit. The study is divided into three aspects. The first is aimed at demonstrating fabrication processes of nanoscale FETs of graphene and porphyrinoid composites based entirely on scanning probe lithography (SPL). A nanoshaving mechanism was used to define patterns on octadecanethiol self-assembled monolayers on gold film evaporated on graphene flakes, followed by metal wet etching and/or oxygen plasma etching to develop patterns on Au films and graphene, respectively. The integrity and optoelectronic properties were examined to validate the processes. The second area of study focused on the development of the chemical sensing platform, enabling chemical changes to be monitored during charge transports under an ambient environment. The localized Raman enhancement was induced by exciting surface plasmon resonance in nanoscale silver enhancing probes made by thermal silver evaporation on sharp AFM tips. As the system was designed along an off-axis illumination/collection scheme, it was demonstrated that it was capable of observing molecular decomposition on opaque and conductive substrates induced by an electric bias. The third line of work proposed a novel TERS system and a probe preparation method. Silver nanowires mounted on AFM tips were used to locally enhance the Raman scattering. The observed Raman enhancement allows quick chemical analysis from a nanoscale region, and thus enables chemical mapping beyond the diffraction limit. Compared with other TERS geometries, the new optical design not only allows analysis on large or opaque samples, but also simplifies the design of the optical components and the alignment processes of the setup.

Collagen fibrils are the main constituent of the extracellular matrix surrounding eukaryotic cells. Even though the assembly and structure of collagen fibrils is well characterized, very little is known about the physico-chemical properties of their surface which is one of the key determinants of their biological functions. One way to obtain surface sensitive structural and chemical data is to take advantage of the near field nature of surface and tip-enhanced Raman spectroscopy. Using Ag and Au nanoparticles bound to collagen type I fibrils, as well as tips coated with a Ag nanoparticles and a thin layer of Ag, we obtained Raman spectra characteristic of the first layer of collagen molecules at the surface of the fibrils. The most frequent Raman peaks were attributed to aromatic residues such as phenylalanine and tyrosine. We also observed in several instances Amide I bands with a full width at half maximum of 10-30 cm-1. The assignment of these Amide I bands positions suggests the presence of collagen-helices as well as alpha-helices and beta-sheets at the fibril’s surface. As a step towards in vivo characterization of collagen fibrils, fascicles removed from tendons were also examined with surface-enhanced Raman spectroscopy.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19724号 / 工博第4179号 / 新制||工||1644(附属図書館) / 32760 / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 平尾 一之, 教授 三浦 清貴, 教授 田中 勝久 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

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Protein structures (cytochrome c) were visualized by TERS measurements on whole mitochondria referring to specific spectral features describing the electronic state of the heme moiety. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Pour mieux comprendre leurs propriétés, diverses nanostructures individuelles ont été étudiées à l’aide d’une technique couplant microscopie à force atomique et spectroscopie Raman confocale. Sous excitation lumineuse polarisée, la composition chimique, la structure et la présence de défauts a pu être précisée dans des nanobâtonnets d’oxydes métalliques (ZnO et α-Fe2O3). Sous irradiation laser résonnante, les spectres de nanotubes de carbone monoparoi enrobés de polymères ont révélé notamment l’absence de transfert de charge polymère-nanotube et un effet de désolvatation. Finalement, des feuillets de graphène oxydé et des ADNs double-brin peignés ont pu être préparés et caractérisés par spectroscopie Raman exaltée par effet de pointe en atteignant une résolution spatiale latérale voisine du rayon de courbure de l’apex de la pointe utilisée (12 nm), bien plus faible que la limite de diffraction, ce qui ouvre la voie à de nouveaux travaux spectroscopiques à l’échelle nanométrique. / To better understand their properties, various nanostructures have been studied using a technique combining atomic force microscopy and confocal Raman spectroscopy. Under polarized light excitation, the chemical composition, the structure and the presence of defects has been described in metal oxides nanorods (ZnO et α-Fe2O3). Under resonant laser excitation, Raman spectra of polymer-wrapped single-walled carbon nanotubes have revealed the absence of polymer-nanotube charge transfer and an effect due to desolvation. Finally, graphene oxide sheets and combed double-stranded DNAs have been prepared and characterized using tip-enhanced Raman spectroscopy with a lateral spatial resolution down to the curvature radius of the apex of the used tip (12 nm), well below the diffraction limit, which opens new opportunities for spectroscopic works at the nanometer scale.

The polymeric gel-forming mucins provide the structural framework of saliva and the mucus barriers that cover the mucosal surfaces of the alimentary canal. Dietary compounds may influence the barrier properties of these protective layers. The effects of green tea polyphenols, which have many health benefits but have low bioavailability and contribute to the astringency of green tea, on the structural properties of the mucins in the alimentary canal are investigated here. Using well characterised, highly purified salivary mucins MUC5B and MUC7, and porcine gastric mucins, the effects of the green tea polyphenol epigallocatechin-3-gallate (EGCG) on mucins were studied here. Using rate-zonal centrifugation coupled to agarose gel electrophoresis, atomic force microscopy and particle tracking microrheology, EGCG, at concentrations found in a cup of green tea, caused increased aggregation of MUC5B in human whole saliva, and increased aggregation and viscosity of purified MUC5B. It was revealed using recombinant proteins of the N- and C-terminal regions of MUC5B that EGCG had these effects by aggregating the terminal globular protein domains of MUC5B. In contrast, MUC5B trypsin-resistant high molecular weight glycopeptides were not aggregated by EGCG, demonstrating that the oligosaccharide-rich, highly-glycosylated regions of mucins are not involved in the EGCG-induced aggregation of mucins. EGCG also caused the majority of MUC7 in human whole saliva to aggregate, and purified MUC7 also showed substantial aggregation in the presence of EGCG.Porcine gastric mucins were also used in order to model human gastric mucins. First, the identity of the porcine gastric mucins was explored using tandem mass spectrometry and immunohistochemistry. This revealed that Muc5ac was expressed by the surface epithelium and was the prominent mucin in porcine gastric mucus. Muc6 was expressed by gastric submucosal glands, but was not a major component of the secreted mucus barrier. Porcine Muc5ac and Muc6 were shown to be aggregated by EGCG. These data demonstrate that mucins from both saliva and the stomach are substantially altered by EGCG. This may contribute to the astringency and low bioavailability of EGCG. In contrast, the green tea polyphenol epicatechin (EC) did not cause aggregation of salivary mucins or porcine gastric mucins, suggesting that the galloyl ring of EGCG (which is absent in EC) is important for its aggregation of mucins, and that EC has different mechanisms of astringency. The structure of the mucins in the alimentary canal was studied using Raman spectroscopy, Raman optical activity (ROA) and Tip-enhanced Raman spectroscopy (TERS). The secondary structure of the oligosaccharide-rich regions of mucins was shown to be largely disordered, with some contribution of poly-proline II helix. The N- and C-terminal regions of MUC5B were largely β-sheet in structure, with some disordered structure also present in the C-terminal region. Raman spectroscopy could reliably distinguish between MUC5B glycoforms, demonstrating the sensitivity of this technique to mucin glycosylation and secondary structure. The first TERS spectra along the length of a MUC5B chain are reported, and suggest that patterns may exist in the glycosylation of MUC5B. Therefore, Raman spectroscopies are novel tools that shed new light on mucin structure and in future may be useful for studying the changes to mucin structure during interactions, such as those with polyphenols.

Protein structures (cytochrome c) were visualized by TERS measurements on whole mitochondria referring to specific spectral features describing the electronic state of the heme moiety. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

La concentration locale des messagers chimiques sécrétés par les cellules peut être mesurée afin de mieux comprendre les mécanismes moléculaires liés à diverses maladies, dont les métastases du cancer. De nouvelles techniques analytiques sont requises pour effectuer ces mesures locales de marqueurs biologiques à proximité des cellules. Ce mémoire présentera le développement d’une nouvelle technique basée sur la réponse plasmonique sur des leviers AFM, permettant d’étudier les réactions chimiques et biologiques à la surface des leviers grâce au phénomène de résonance des plasmons de surface (SPR), ainsi qu’à la diffusion Raman exaltée par effet de pointe (TERS). En effet, il est possible de localiser l’amplification du signal Raman à la pointe d’un levier AFM, tout comme le principe de la diffusion Raman exaltée par effet de surface (SERS) basée sur la diffusion de la lumière par des nanoparticules métalliques, et permettant une large amplification du signal Raman. La surface du levier est recouverte d’une nano-couche métallique d’or, suivi par des réactions biologiques pour l’immobilisation d’un récepteur moléculaire, créant ainsi un biocapteur sur la pointe du levier. Une détection secondaire utilisant des nanoparticules d’or conjuguées à un anticorps secondaire permet également une amplification du signal SPR et Raman lors de la détection d’antigène. Ce mémoire démontrera le développement et la validation de la détection de l’immunoglobuline G (IgG) sur la pointe du levier AFM.Dans des projets futurs, cette nouvelle technique d’instrumentation et d’imagerie sera optimisée grâce à la création d’un micro-détecteur protéique généralement adapté pour l’étude de la communication cellulaire. En intégrant le signal SPR à la microscopie AFM, il sera alors possible de développer des biocapteurs SPR couplés à une sonde à balayage, ce qui permettra d’effectuer une analyse topographique et de l’environnement chimique d’échantillons cellulaires en temps réel, pour la mesure des messagers moléculaires sécrétés dans la matrice extracellulaire, lors de la communication cellulaire. / Measurement of the local concentration of chemical messengers secreted by cells may give a better understanding of molecular mechanisms related to different diseases, such as cancer metastasis. Current techniques are not suited to perform such measurements and thus, new analytical techniques must be developed. This Master’s thesis reports the development of a new technique based on the plasmonic response of atomic force microscopy (AFM) tips, which will ultimately allow monitoring of chemical and biological molecules on the surface of a cantilever by use of surface plasmon resonance (SPR) and tip-enhanced Raman scattering (TERS). Indeed, it is possible to localize the enhancement of the Raman signal on the AFM tip using principles associated to surface-enhanced Raman spectroscopy (SERS), based on the absorption of light by nanometer-sized metal particles, resulting in a large enhancement of the Raman signal. The AFM tip was constructed by the deposition of a nanometer-size gold layer, followed by the assembly of a biosensor with a biomolecular receptor. Gold nanoparticles (AuNPs) conjugated with a secondary antibody served as the secondary detection step. In addition, the use of the gold nanoparticles for antigen detection allows an amplification of the SPR and Raman signals. This Master’s thesis will demonstrate the development and validation of a biosensor for immunoglobuline G (IgG) at the tip of an AFM cantilever.This thesis sets the basis for future projects, where this new imaging technique will be developed for monitoring cellular communication by exploiting the plasmonic signal at the AFM tip. Different biosensors will then be developed and coupled to an AFM probe for scanning the chemical environment and detect in real-time chemical messengers secreted in the extracellular matrix in cellular communication.