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- ItemSecondary Structure and Glycosylation of Mucus Glycoproteins by Raman Spectroscopies(Columbus, Ohio : American Chemical Society, 2016) Davies, Heather S.; Singh, Prabha; Deckert-Gaudig, Tanja; Deckert, Volker; Rousseau, Karine; Ridley, Caroline E.; Dowd, Sarah E.; Doig, Andrew J.; Pudney, Paul D. A.; Thornton, David J.; Blanch, Ewan W.The major structural components of protective mucus hydrogels on mucosal surfaces are the secreted polymeric gel-forming mucins. The very high molecular weight and extensive O-glycosylation of gel-forming mucins, which are key to their viscoelastic properties, create problems when studying mucins using conventional biochemical/structural techniques. Thus, key structural information, such as the secondary structure of the various mucin subdomains, and glycosylation patterns along individual molecules, remains to be elucidated. Here, we utilized Raman spectroscopy, Raman optical activity (ROA), circular dichroism (CD), and tip-enhanced Raman spectroscopy (TERS) to study the structure of the secreted polymeric gel-forming mucin MUC5B. ROA indicated that the protein backbone of MUC5B is dominated by unordered conformation, which was found to originate from the heavily glycosylated central mucin domain by isolation of MUC5B O-glycan-rich regions. In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D′-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. Using these findings, we employed TERS, which combines the chemical specificity of Raman spectroscopy with the spatial resolution of atomic force microscopy to study the secondary structure along 90 nm of an individual MUC5B molecule. Interestingly, the molecule was found to contain a large amount of α-helix/unordered structures and many signatures of glycosylation, pointing to a highly O-glycosylated region on the mucin.
- ItemDetection of Protein Glycosylation Using Tip-Enhanced Raman Scattering(Columbus, Ohio : American Chemical Society, 2016) Cowcher, David P.; Deckert-Gaudig, Tanja; Brewster, Victoria L.; Ashton, Lorna; Deckert, Volker; Goodacre, RoystonThe correct glycosylation of biopharmaceutical glycoproteins and their formulations is essential for them to have the desired therapeutic effect on the patient. It has recently been shown that Raman spectroscopy can be used to quantify the proportion of glycosylated protein from mixtures of native and glycosylated forms of bovine pancreatic ribonuclease (RNase). Here we show the first steps toward not only the detection of glycosylation status but the characterization of glycans themselves from just a few protein molecules at a time using tip-enhanced Raman scattering (TERS). While this technique generates complex data that are very dependent on the protein orientation, with the careful development of combined data preprocessing, univariate and multivariate analysis techniques, we have shown that we can distinguish between the native and glycosylated forms of RNase. Many glycoproteins contain populations of subtly different glycoforms; therefore, with stricter orientation control, we believe this has the potential to lead to further glycan characterization using TERS, which would have use in biopharmaceutical synthesis and formulation research.
- ItemControl of the emission wavelength of gallium nitride-based nanowire light-emitting diodes(Berlin : Humboldt-Universität zu Berlin, 2013) Wölz, MartinHalbleiter-Nanosäulen (auch -Nanodrähte) werden als Baustein für Leuchtdioden (LEDs) untersucht. Herkömmliche LEDs aus Galliumnitrid (GaN) bestehen aus mehreren Kristallschichten auf einkristallinen Substraten. Ihr Leistungsvermögen wird durch Gitterfehlpassung und dadurch hervorgerufene Verspannung, piezoelektrische Felder und Kristallfehler beschränkt. GaN-Nanosäulen können ohne Kristallfehler auf Fremdsubstraten gezüchtet werden. Verspannung wird in Nanosäulen elastisch an der Oberfläche abgebaut, dadurch werden Kristallfehler und piezoelektrische Felder reduziert. In dieser Arbeit wurden GaN-Nanosäulen durch Molukularstrahlepitaxie katalysatorfrei gezüchtet. Eine Machbarkeitsstudie über das Kristallwachstum von Halbleiter-Nanosäulen auf Metall zeigt, dass GaN-Nanosäulen in hoher Kristallqualität ohne einkristallines Substrat epitaktisch auf Titanschichten gezüchtet werden können. Für das Wachstum axialer (In,Ga)N/GaN Heterostrukturen in Nanosäulen wurden quantitative Modelle entwickelt. Die erfolgreiche Herstellung von Nanosäulen-LEDs auf Silizium-Wafern zeigt, dass dadurch eine Kontrolle der Emissionswellenlänge erreicht wird. Die Gitterverspannung der Heterostrukturen in Nanosäulen ist ungleichmäßig aufgrund des Spannungsabbaus an den Seitenwänden. Das katalysatorfreie Zuchtverfahren führt zu weiteren statistischen Schwankungen der Nanosäulendurchmesser und der Abschnittlängen. Die entstandene Zusammensetzung und Verspannung des (In,Ga)N-Mischkristalls wird durch Röntgenbeugung und resonant angeregte Ramanspektroskopie ermittelt. Infolge der Ungleichmäßigkeiten erfordert die Auswertung genaue Simulationsrechnungen. Eine einfache Näherung der mittleren Verspannung einzelner Abschnitte kann aus den genauen Rechnungen abgeleitet werden. Gezielte Verspannungseinstellung erfolgt durch die Wahl der Abschnittlängen. Die Wirksamkeit dieses allgemeingültigen Verfahrens wird durch die Bestimmung der Verspannung von (In,Ga)N-Abschnitten in GaN-Nanosäulen gezeigt.
- ItemEpitaxial growth and characterization of GeTe and GeTe/Sb2Te3 superlattices(Berlin : Humboldt-Universität zu Berlin, 2017) Wang, Rui NingDie epitaktische Wachstum von GeTe Dünnschichten und Sb2Te3/GeTe Übergittern durch Molekularstrahlepitaxie wird auf drei verschiedenen Silizium Oberflächen gezeigt: Si(111)−(7×7), Si(111)−(√3×√3)R30°−Sb, und Si(111)−(1×1)−H. Mit Röntgenstrukturanalyse wird bewiesen, dass die epitaktische Beziehung der GeTe Schicht von der Oberflächepassievierung abhängig ist; auf einer passivierten Fläche können verdrehte Domänen unterdrückt sein. Dieses Verhalten ähnelt dem, welches bei 2D Materialien zu erwarten wäre, und wird auf die Schwäche der Resonanten ungebundenen Zustände zurückgeführt, die durch Peierls Verzerrung noch schwächer werden.
- ItemAutomatic spike correction using UNIFIT 2020(Chichester [u.a.] : Wiley, 2019) Hesse, Ronald; Bundesmann, Carsten; Denecke, ReinhardThe improvement of the software UNIFIT 2020 from an analysis processing software for photoelectron spectroscopy (XPS) only to a powerful tool for XPS, Auger electron spectroscopy (AES), X-ray absorption spectroscopy (XAS), and Raman spectroscopy requires new additional programme routines. Particularly, the implementation of the analysis of Raman spectra needs a well-working automatic spike correction. The application of the modified discrete Laplace operator method allows for a perfect localization and correction of the spikes and finally a successful peak fit of the spectra. The theoretical basis is described. Test spectra allow for the evaluation of the presented method. A comparison of the original and spike-corrected real measurements demonstrates the high quality of the method used.
- ItemMonitoring conical intersections in the ring opening of furan by attosecond stimulated X-ray Raman spectroscopy(Melville, NY : AIP Publishing LLC, 2015) Hua, Weijie; Oesterling, Sven; Biggs, Jason D.; Zhang, Yu; Ando, Hideo; de Vivie-Riedle, Regina; Fingerhut, Benjamin P.; Mukamel, ShaulAttosecond X-ray pulses are short enough to capture snapshots of molecules undergoing nonadiabatic electron and nuclear dynamics at conical intersections (CoIns). We show that a stimulated Raman probe induced by a combination of an attosecond and a femtosecond pulse has a unique temporal and spectral resolution for probing the nonadiabatic dynamics and detecting the ultrafast (∼4.5 fs) passage through a CoIn. This is demonstrated by a multiconfigurational self-consistent-field study of the dynamics and spectroscopy of the furan ring-opening reaction. Trajectories generated by surface hopping simulations were used to predict Attosecond Stimulated X-ray Raman Spectroscopy signals at reactant and product structures as well as representative snapshots along the conical intersection seam. The signals are highly sensitive to the changes in nonadiabatically coupled electronic structure and geometry.
- ItemIsotropic multi-gap superconductivity in BaFe1.9Pt0.1As2 from thermal transport and spectroscopic measurements(Bristol : IOP Publishing, 2014) Ziemak, Steven; Kirshenbaum, K.; Saha, S.R.; Hu, R.; Reid, J.-Ph.; Gordon, R.; Taillefer, L.; Evtushinsky, D.; Thirupathaiah, S.; Büchner, B.; Borisenko, S.V.; Ignatov, A.; Kolchmeyer, D.; Blumberg, G.; Paglione, J.Thermal conductivity, point contact spectroscopy, angle-resolved photoemission and Raman spectroscopy measurements were performed on BaFe1.9Pt0.1As2 single crystals obtained from the same synthesis batch in order to investigate the superconducting energy gap structure using multiple techniques. Low temperature thermal conductivity was measured in the superconducting state as a function of temperature and magnetic field, revealing an absence of quasiparticle excitations in the $T\to 0$ limit up to 15 T applied magnetic fields. Point-contact Andreev reflection spectroscopy measurements were performed as a function of temperature using the needle-anvil technique, yielding features in the conductance spectra at both 2.5 meV and 7.0 meV scales consistent with a multi-gap scenario. Angle-resolved photoemission spectroscopy probed the electronic band structure above and below the superconducting transition temperature of Tc = 23 K, revealing an isotropic gap of magnitude $\sim 3$ meV on both electron and hole pockets. Finally, Raman spectroscopy was used to probe quasiparticle excitations in multiple channels, showing a threshold energy scale of 3 meV below Tc. Overall, we find strong evidence for an isotropic gap structure with no nodes or deep minima in this system, with a 3 meV magnitude gap consistently observed and a second, larger gap suggested by point-contact spectroscopy measurements. We discuss the implications that the combination of these results reveal about the superconducting order parameter in the BaFe2−xPtxAs2 doping system and how this relates to similar substituted iron pnictides.
- ItemFar-infrared and Raman spectroscopy investigation of phonon modes in amorphous and crystalline epitaxial GeTe-Sb2Te3 alloys(London : Nature Publishing Group, 2016) Bragaglia, V.; Holldack, K.; Boschker, J.E.; Arciprete, F.; Zallo, E.; Flissikowski, T.; Calarco, R.A combination of far-infrared and Raman spectroscopy is employed to investigate vibrational modes and the carrier behavior in amorphous and crystalline ordered GeTe-Sb2Te3 alloys (GST) epitaxially grown on Si(111). The infrared active GST mode is not observed in the Raman spectra and vice versa, indication of the fact that inversion symmetry is preserved in the metastable cubic phase in accordance with the Fm3 space group. For the trigonal phase, instead, a partial symmetry break due to Ge/Sb mixed anion layers is observed. By studying the crystallization process upon annealing with both the techniques, we identify temperature regions corresponding to the occurrence of different phases as well as the transition from one phase to the next. Activation energies of 0.43 eV and 0.08 eV for the electron conduction are obtained for both cubic and trigonal phases, respectively. In addition a metal-insulator transition is clearly identified to occur at the onset of the transition between the disordered and the ordered cubic phase.
- ItemDistinction of nucleobases - A tip-enhanced Raman approach(Frankfurt, M. : Beilstein-Institut zur Förderung der Chemischen Wissenschaften, 2011) Treffer, R.; Lin, X.; Bailo, E.; Deckert-Gaudig, T.; Deckert, V.The development of novel DNA sequencing methods is one of the ongoing challenges in various fields of research seeking to address the demand for sequence information. However, many of these techniques rely on some kind of labeling or amplification steps. Here we investigate the intrinsic properties of tip-enhanced Raman scattering (TERS) towards the development of a novel, label-free, direct sequencing method. It is known that TERS allows the acquisition of spectral information with high lateral resolution and single-molecule sensitivity. In the presented experiments, single stranded adenine and uracil homopolymers were immobilized on different kinds of substrates (mica and gold nanoplates) and TERS experiments were conducted, which demonstrated the reproducibility of the technique. To elucidate the signal contributions from the specific nucleobases, TERS spectra were collected on single stranded calf thymus DNA with arbitrary sequence. The results show that, while the Raman signals with respect to the four nucleobases differ remarkably, specific markers can be determined for each respective base. The combination of sensitivity and reproducibility shows that the crucial demands for a sequencing procedure are met.
- ItemTowards multiple readout application of plasmonic arrays(Frankfurt, M. : Beilstein-Institut zur Förderung der Chemischen Wissenschaften, 2011) Cialla, D.; Weber, K.; Böhme, R.; Hübner, U.; Schneidewind, H.; Zeisberger, M.; Mattheis, R.; Möller, R.; Popp, J.In order to combine the advantages of fluorescence and surface-enhanced Raman spectroscopy (SERS) on the same chip platform, a nanostructured gold surface with a unique design, allowing both the sensitive detection of fluorescence light together with the specific Raman fingerprint of the fluorescent molecules, was established. This task requires the fabrication of plasmonic arrays that permit the binding of molecules of interest at different distances from the metallic surface. The most efficient SERS enhancement is achieved for molecules directly adsorbed on the metallic surface due to the strong field enhancement, but where, however, the fluorescence is quenched most efficiently. Furthermore, the fluorescence can be enhanced efficiently by careful adjustment of the optical behavior of the plasmonic arrays. In this article, the simultaneous application of SERS and fluorescence, through the use of various gold nanostructured arrays, is demonstrated by the realization of a DNA detection scheme. The results shown open the way to more flexible use of plasmonic arrays in bioanalytics.