Lysosomen spielen entscheidende Rolle bei der zellulären Homöostase. Die Überwachung von Lysosomen, die Lipide ansammeln, ist eine erhebliche Herausforderung. Diese Arbeit konzentriert sich auf die Entwicklung der oberflächenverstärkten Raman-Streuung (SERS) als Methode zur Überwachung intakter Lysosomen, insbesondere hinsichtlich des Einflusses von Arzneimitteln, die den Lipidstoffwechsel stören. Um das Potenzial von SERS zur Untersuchung von Lysosomen in lebenden Zellen zu bewerten, wurden die Wechselwirkungen zwischen trizyklischen Antidepressiva und saurer Sphingomyelinase untersucht. Zunächst wurden Modellsysteme untersucht. Die Wechselwirkungen zwischen den Antidepressiva und Goldnanopartikeln wurden durch SERS charakterisiert. Die Daten zeigten, dass Moleküle mit den Nanopartikeln interagieren. Als Modellsystem der lipidreichen Umgebung wurden Komposite aus Liposomen und Goldnanopartikeln von SERS und Cryo-EM untersucht. Die SERS-Spektren sind charakteristisch für die Lipidzusammensetzung der Vesikel. Die Wechselwirkungen zwischen den Antidepressiva und den Lysosomen wurden in der Fibroblastenzelllinie 3T3 durch SERS und komplementäre Methoden untersucht. In Übereinstimmung mit den SERS-Spektren von Modellsystemen zeigen die SERS-Spektren lebender Zellen Signaturen sowohl der Antidepressiva als auch der Lipide. Um die Unterschiede in den Lysosomen zwischen behandelten und nicht behandelten Zellen aufzudecken, wurde ein zufälliger Waldansatz verwendet. Darüber hinaus wurde SERS verwendet, um die Lipidverteilung in Leishmania-infizierten Makrophagen zu untersuchen, von denen bekannt ist, dass sie Lipide akkumulieren. Die Ergebnisse zeigen, dass SERS verwendet werden kann, um die Lipidzusammensetzung in lebenden Zellen verschiedener Zelltypen zu untersuchen. Als neue methodische Entwicklung zeigt die Random-Forest-Analyse von SERS-Daten, dass Ansätze des maschinellen Lernens für ein besseres Verständnis von Daten aus biologischen Systemen nützlich sein können. / Lysosomes play a crucial role in cellular homeostasis. Monitoring lysosomes that accumulate lipids represents a considerable challenge. This thesis focuses on the development of surface-enhanced Raman scattering (SERS) as a method to monitor intact lysosomes, in particular regarding the influence of drugs that interfere with lipid metabolism. To evaluate the potential of SERS for studying lysosomes in live cells, the interactions between tricyclic antidepressants and acid sphingomyelinase were studied. First, model systems were investigated. The interactions between the antidepressants and gold nanoparticles were characterized by SERS. The data showed that molecules interact with the nanoparticles. As a model system of the lipid-rich environment, composites of liposome and gold nanoparticles were studied by SERS and cryo-EM. The SERS spectra are characteristic of the vesicles’ lipid composition. The interactions between the antidepressants and the lysosomes were studied in the fibroblast cell line 3T3 by SERS and complementary methods. In agreement with the SERS spectra of model systems, the SERS spectra of live cells show signatures of both, the antidepressants and the lipids. To reveal the differences in the lysosomes between treated and non-treated cells, a random forest approach was used. Moreover, SERS was used to study the lipid distribution in Leishmania-infected macrophages known to accumulate lipids. The results show that SERS can be used to investigate lipid composition in live cells of different cell types. As a new methodological development, the random forest analysis of SERS data shows that machine learning approaches can be useful for a better understanding of data from biological systems.

Nanopartikel basierte colorimetrische Assays bieten vielfältige Anwendungsmöglichkeiten vom Nachweis ionischer oder molekularer Spezies bis hin zu komplexen Strukturen, wie zum Beispiel Zellen oder Bakterien. Trotz der großen Anzahl von Anwendungsbeispielen in der Literatur gibt es nur sehr wenige Beispiele für den Fall, wenn Analyt und Sensorpartikel etwa gleich groß sind. Jedoch nimmt das Interesse an dem Nachweis solcher Analyten, wie zum Beispiel von Viren, in der Bioverfahrenstechnik, der Umwelttechnik und Medizin stetig zu. In der Dissertation wird anhand von drei unterschiedlichen Anwendungsbeispielen die lückenlose Anwendbarkeit des Nanopartikel basierten colorimetrischen Sensorprinzips für verschiedene Analyten aus dem gesamten interessierenden Größenspektrum nachgewiesen. Für die Detektion von Ionen bzw. Ionenkomplexen ist mit der Funktionalisierung der Goldnanopartikel mit bakteriellen Zellhüllenproteinen ein spezifisches Nachweisverfahren für spezielle Ionenkomplexe entwickelt worden. Erste Ergebnisse zum Nachweis von toxischen Arsen(V)-Komplexen in wässriger Lösung belegen das enorme Potential. Als Nachweisgrenze konnten Werte im Bereich herkömmlicher sensitiver Messverfahren ermittelt werden. Durch Untersuchung der Wechselwirkung von Au- und AuxAg1-x–Nanopartikeln mit dendritischen Polymerstrukturen mit Abmessungen im Größenbereich zwischen 2 und 5 nm konnten tiefere Einblicke in das Aggregationsverhalten der Partikel bei der Ausbildung größerer komplexer Strukturen erzielt werden, die eine sensorische Umsetzung ermöglichen. Derartige Betrachtungen existieren bisher nur für Ionen oder kleinere molekulare Spezies. Der Nachweis von Analyten mit zu den Nanopartikeln vergleichbarer Größe wird am Beispiel zweier unterschiedlicher viraler Proben, dem Rinder-Coronavirus (BCV) und einem humanen Influenzavirus (H3N2) in grundlegenden Experimenten demonstriert. Die Durchführung dieser Arbeiten mit prozessnahem Virusprobenmaterial ist mit besonderen Herausforderungen an die Signalgewinnung und Interpretation verbunden. Aufbauend auf diesen experimentellen Ergebnissen konnte in einer skalenübergreifenden Betrachtung für Analytgrößen vom Subnanometerbereich bis hin zu einigen hundert Nanometern die lückenlose, universelle Anwendbarkeit des colorimetrischen Sensorprinzips demonstriert werden. Diese Betrachtungen ermöglichen generelle Aussagen zur Lage des Farbumschlagbereiches sowohl in Abhängigkeit von der Analytgröße als auch der Funktionalisierung, der Konzentration und der Größe der Nanopartikel.

Movement of motor proteins along cytoskeletal filaments is fundamental for various cellular processes ranging from muscle contraction over cell division and flagellar movement to intracellular transport. Not surprisingly, the impairment of motility was shown to cause severe diseases. For example, a link between impaired intracellular transport and neurodegenerative diseases, such as Alzheimer’s, has been established. There, the movement of kinesin-1, a neuronal motor protein transporting vesicles along microtubules toward the axonal terminal, is thought to be strongly affected by roadblocks leading to malfunction and death of the nerve cell. Detailed information on how the motility of kinesin-1 deteriorates in the presence of roadblocks and whether the motor has a mechanism to circumvent such obstructions is scarce. In this thesis, kinesin-1 motility was studied in vitro in the presence of rigor kinesin-1 mutants, which served as permanent roadblocks, under controlled single-molecule conditions. The 25 nm wide microtubule track, consisting of 13 individual protofilaments, resembles a multi-lane environment for transport by processive kinesin-1 motors. The existence of multiple traffic-lanes, allows kinesin-1 to utilize different paths for cargo transport and potentially also for the circumvention of roadblocks. However, direct observation of motor encounters with roadblocks has been intricate in the past, mainly due to limitations in both, spatial and temporal resolution. These limitations, intrinsic to fluorescent probes commonly utilized to report on the motor positions, originate from a low rate of photon generation (low brightness) and a limited photostability (short observation time). Thus, studying kinesin-1 encounters with microtubule-associated roadblocks requires alternative labels, which explicitly avoid the shortcomings of fluorescence and consequently allow for a higher localization precision. Promising candidates for replacing fluorescent dyes are gold nanoparticles (AuNPs), which offer an enormous scattering cross-section due to plasmon resonance in the visible part of the optical spectrum. Problematic, however, is their incorporation into conventionally used (fluorescence) microscopes, because illumination and scattered light have the same wavelength and cannot be separated spectrally. Therefore, an approach based on total internal reflection (TIR) utilizing a novel parabolically shaped quartz prism for illumination was developed within this thesis. This approach provided homogenous and spatially invariant illumination profiles in combination with a convenient control over a wide range of illumination angles. Moreover, single-molecule fluorescence as well as single-particle scattering were detectable with high signal-to-noise ratios. Importantly, AuNPs with a diameter of 40 nm provided sub-nanometer localization accuracies within millisecond integration times and reliably reported on the characteristic 8 nm stepping of individual kinesin-1 motors moving along microtubules. These results highlight the potential of AuNPs to replace fluorescent probes in future single-molecule experiments. The newly developed parabolic prism-type TIR microscope is expected to strongly facilitate such approaches in the future. To study how the motility of kinesin-1 is affected by permanent roadblocks on the microtubule lattice, first, conventional objective-type TIRF microscopy was applied to GFP-labeled motors. An increasing density of roadblocks caused the mean velocity, run length, and dwell time to decrease exponentially. This is explained by (i) the kinesin-1 motors showing extended pausing phases when confronted with a roadblock and (ii) the roadblocks causing a reduction in the free path of the motors. Furthermore, kinesin-1 was found to be highly sensitive to the crowdedness of microtubules as a roadblock decoration as low as 1 % sufficed to significantly reduce the landing rate. To study events, where kinesin-1 molecules continued their runs after having paused in front of a roadblock, AuNPs were loaded onto the tails of the motors. When observing the kinesin-1 motors with nanometer-precision, it was interestingly found that about 60 % of the runs continued by movements to the side, with the left and right direction being equally likely. This finding suggests that kinesin-1 is able to reach to a neighboring protofilament in order to ensure ongoing transportation. In the absence of roadblocks, individual kinesin-1 motors stepped sideward with a much lower, but non-vanishing probability (0.2 % per step). These findings suggest that processive motor proteins may possess an intrinsic side stepping mechanism, potentially optimized by evolution for their specific intracellular tasks.

Movement of motor proteins along cytoskeletal filaments is fundamental for various cellular processes ranging from muscle contraction over cell division and flagellar movement to intracellular transport. Not surprisingly, the impairment of motility was shown to cause severe diseases. For example, a link between impaired intracellular transport and neurodegenerative diseases, such as Alzheimer’s, has been established. There, the movement of kinesin-1, a neuronal motor protein transporting vesicles along microtubules toward the axonal terminal, is thought to be strongly affected by roadblocks leading to malfunction and death of the nerve cell. Detailed information on how the motility of kinesin-1 deteriorates in the presence of roadblocks and whether the motor has a mechanism to circumvent such obstructions is scarce. In this thesis, kinesin-1 motility was studied in vitro in the presence of rigor kinesin-1 mutants, which served as permanent roadblocks, under controlled single-molecule conditions. The 25 nm wide microtubule track, consisting of 13 individual protofilaments, resembles a multi-lane environment for transport by processive kinesin-1 motors. The existence of multiple traffic-lanes, allows kinesin-1 to utilize different paths for cargo transport and potentially also for the circumvention of roadblocks. However, direct observation of motor encounters with roadblocks has been intricate in the past, mainly due to limitations in both, spatial and temporal resolution. These limitations, intrinsic to fluorescent probes commonly utilized to report on the motor positions, originate from a low rate of photon generation (low brightness) and a limited photostability (short observation time). Thus, studying kinesin-1 encounters with microtubule-associated roadblocks requires alternative labels, which explicitly avoid the shortcomings of fluorescence and consequently allow for a higher localization precision. Promising candidates for replacing fluorescent dyes are gold nanoparticles (AuNPs), which offer an enormous scattering cross-section due to plasmon resonance in the visible part of the optical spectrum. Problematic, however, is their incorporation into conventionally used (fluorescence) microscopes, because illumination and scattered light have the same wavelength and cannot be separated spectrally. Therefore, an approach based on total internal reflection (TIR) utilizing a novel parabolically shaped quartz prism for illumination was developed within this thesis. This approach provided homogenous and spatially invariant illumination profiles in combination with a convenient control over a wide range of illumination angles. Moreover, single-molecule fluorescence as well as single-particle scattering were detectable with high signal-to-noise ratios. Importantly, AuNPs with a diameter of 40 nm provided sub-nanometer localization accuracies within millisecond integration times and reliably reported on the characteristic 8 nm stepping of individual kinesin-1 motors moving along microtubules. These results highlight the potential of AuNPs to replace fluorescent probes in future single-molecule experiments. The newly developed parabolic prism-type TIR microscope is expected to strongly facilitate such approaches in the future. To study how the motility of kinesin-1 is affected by permanent roadblocks on the microtubule lattice, first, conventional objective-type TIRF microscopy was applied to GFP-labeled motors. An increasing density of roadblocks caused the mean velocity, run length, and dwell time to decrease exponentially. This is explained by (i) the kinesin-1 motors showing extended pausing phases when confronted with a roadblock and (ii) the roadblocks causing a reduction in the free path of the motors. Furthermore, kinesin-1 was found to be highly sensitive to the crowdedness of microtubules as a roadblock decoration as low as 1 % sufficed to significantly reduce the landing rate. To study events, where kinesin-1 molecules continued their runs after having paused in front of a roadblock, AuNPs were loaded onto the tails of the motors. When observing the kinesin-1 motors with nanometer-precision, it was interestingly found that about 60 % of the runs continued by movements to the side, with the left and right direction being equally likely. This finding suggests that kinesin-1 is able to reach to a neighboring protofilament in order to ensure ongoing transportation. In the absence of roadblocks, individual kinesin-1 motors stepped sideward with a much lower, but non-vanishing probability (0.2 % per step). These findings suggest that processive motor proteins may possess an intrinsic side stepping mechanism, potentially optimized by evolution for their specific intracellular tasks.

Noble metal nanoparticles have attracted the attentions of many researchers because of unique plasmonic properties since their discovery and successful preparation. Nanocluster formed by the assembly of noble metal nanoparticles can exhibit plasmonic characteristics beyond those of individual nanoparticles, which can be tuned, to a large extent, by adjusting the size, shape, chemical composition, and arrangement of individual nanoparticles. Usually nanocluster with special ordered structures is called as superstructure, which can be designed for different purposes through various methods. Colloidal assembly as a cost-efficient approach can be widely used for fabrication of plasmonic superstructure in solution media. As an introduction of background, the developments of plasmonic nanoparticles and nanoclusters have been discussed in the aspects of their LSPR properties, surface modification for colloidal assembly, and sensing applications. Both colorimetry and SERS detection based on plasmonic assemblies have been presented as effective sensing methods, which are also the motivations for the main experiments in this thesis. As a proof-of-motivation, the different kinds of thiol-terminated PEG assisted hybrid gold nanoparticles have been applied for the protein colorimetric detections based on the specific interaction between heparin and proteins with different surface affinities. In addition, PEG-assisted core/satellite superstructures with various polymer thickness as SERS platform have been demonstrated for trace sensing of specific target molecules in solution. Especially, the method to differentiate between the radiative and non-radiative contributions of plasmonic superstructure has been proposed using diffuse reflectance spectroscopy, which provides a favorable selection and design of best candidates for specific application scenarios. Finally, the concept of NIR-II SERS using biological transparency window has been introduced including the fundamental requirements, which proposed a future experiment to fabricate suitable superstructures for potential biomedical applications with high penetration depth at low laser powers. Generally speaking, the central focus of this thesis is the effect of polymer modification on the structures and properties of plasmonic superstructure and its sensing application. The main research efforts are divided into three parts: (I) investigate the topological effect of polymer structure parameters on plasmonic properties for colorimetric analytics; (II) investigate the impact of interparticle spacing within the assemblies and polymer dimensions on the SERS activity; (III) investigate the plasmonic properties tailoring of superstructures as well as the contribution of scattering (radiative) and absorption (non-radiative), i.e. light-to-heat conversion, within the ensemble optical response.