In this work, a chemiresistor-type sensing platform based on aligned arrays of nitrogen-doped multi-walled carbon nanotubes (N-MWCNTs) was developed. Our N-MWCNT based sensors can be made on both rigid and flexible substrates; they are small, have low power consumption and are suitable for highly efficient and reliable detection of different biomolecules and gases, at room temperature. The performance of these sensors was demonstrated for avian influenza virus (AIV) subtype H5N1 DNA sequences and toxic gases NO and NH3 at low concentrations. In our study, chemical vapor deposition (CVD) method was applied to synthesize vertically aligned nitrogen doped carbon nanotube arrays on a large area (> 1 cm2) on Si/SiO2 substrate using Fe/Al2O3 layer as a catalyst and a mixture of ethanol and acetonitrile as a C/N source. Especially, the diameter, length, nitrogen-doping concentration and morphology of the nanotubes were controllably tailored by adjusting the thickness of catalyst film, reaction duration and temperature as well as the amount of nitrogen-containing precursor. For integrating N-MWCNTs into chemiresistor devices, we developed a direct contact printing method for a dry, controllable and uniform transferring and positioning of the CVD-grown vertical nanotubes onto well-defined areas of various rigid and flexible substrates. After horizontally aligned N-MWCNT arrays were formed on a target substrate, interdigitated metallic microelectrodes with an interspacing of 3 µm were deposited perpendicular to the nanotube alignment direction to fabricate chemiresistor devices for biomolecule and gas sensing. This way, well-aligned nanotubes were laid across the Au/Cr interdigitated electrode fingers, had a strong adhesion with the electrodes and served as conducting channels bridging the electrodes. The N-MWCNT based chemiresistor device was applied as a label-free DNA sensor for a highly sensitive and fast detection of AIV subtype H5N1 DNA sequences. For this, the nanotubes were functionalized with probe DNA, which was non-covalently attached to sidewalls of the N-MWCNTs via π-π interaction. Such functionalized sensors were applied to quantitatively detect complementary DNA target with concentration ranging from 20 pM to 2 nM after 15 min incubation at room temperature. The sensors showed no response to non-complementary DNA target for concentrations up to 2 µM showing an excellent selectivity. Investigations on the efficient gas sensing of N-MWCNT-based chemiresistor of reducing/ oxidizing gases NH3 and NO were also reported in this work. The aim was to assess the possibility for N-MWCNTs to be applied as innovative sensing materials for room temperature gas sensing. N-MWCNTs with varying doping levels (N/C ratio of 5.6 to 9.3at%) were used as sensing materials and exposed to NH3 (1.5-1000 ppm) and NO (50-1000 ppm) for exploring and comparing their sensing performance. This study offered an effective route for further modification of CNTs according to various sensing application. Finally, our investigations showed a high potential of the developed N-MWCNT-based sensing platform for various applications ranging from environmental monitoring to point-of-care medical diagnostics.

This work was performed in the framework of two application-oriented research projects that focus on the generation and evaluation of fluorescent Saccharomyces (S.) cerevisiae-based sensor and reporter cells for white biotechnology as well as the extension of the conventional single-cell/single-construct principle of ordinary yeast biosensor approaches. Numerous products are currently generated by biotechnological processes which require continuous and precise process control and monitoring. These demands are only partially met by physical or physiochemical sensors since they measure parameters off-line or use surrogate parameters that consequently provide only indirect information about the actual process performance. Biosensors, in particular whole cell-based biosensors, have the unique potential to near-line and long-term monitor parameters such as nutrient availability during fermentation processes. Moreover, they allow for the assessment of an analyte’s biological relevance. Prototype yeast sensor and reporter strains derived from common laboratory strains were transformed with multicopy expression plasmids that mediate constitutive or inducible expression of a fluorescence reporter gene. Performance of these cells was examined by various qualitative and quantitative detection methods – representative of putative transducer technologies. Analyses were performed on the population level by microplate reader-based fluorometry and Western blot as well as on the single-cell level by fluorescence microscopy and flow cytometry. ‘Signature’ promoters that are activated or repressed during particular nutrient-limited growth conditions were selected in order to generate yeast nutrient sensor strains for monitoring the biological availability of nitrogen, phosphorus or sulphur. For each category, at least one promoter mediating at least threefold changed green fluorescence levels between sensor cells in non-limited and nutrient-limited conditions was identified. Sensor strains were evaluated in detail regarding sensitivity, analyte selectivity and the ability to restore basic fluorescence after shift from nutrient-limited to non-limited conditions (regeneration). The applicability for bioprocess monitoring purposes was tested by growth of yeast nutrient sensor cells in microalgae media and supernatants. Despite successful proof of principle, numerous challenges still need to be solved to realise prospective implementation in this field of white biotechnology. The major drawback of plasmid-borne detection constructs is a high fluorescence variance between individual cells. By generation of a nitrogen sensor strain with a genome-integrated detection construct, uniform expression on the single-cell level and simultaneous maintenance of basic properties (ability of fluorescence induction/regeneration and lack of cross-reactivity) was achieved. However, due to the singular detection construct per cell, significantly weaker overall fluorescence was observed. The traditional single-cell/single-construct approach was expanded upon in two ways. Firstly, a practical dual-colour sensor strain was created by simultaneous, constitutive expression of a red fluorescence reporter gene in green fluorescent nitrogen sensor cells. Secondly, an innovative cellular communication and signal amplification system inspired by the natural S. cerevisiae pheromone system and mating response was established successfully. It features the yeast pheromone alpha-factor as a trigger and alpha-factor-responsive reporter cells which express a fluorescence reporter gene from the pheromone-inducible FIG1 promoter as an output signal. The system was functional both with synthetic and cell-secreted alpha-factor, provided that recombinant cells were deleted for the alpha-factor protease Bar1p. Integration of amplifier cells which secrete alpha-factor in response to stimulation with the pheromone itself could increase the system\'s sensitivity further. Signal amplification was demonstrated for phosphorus sensor cells as a proof of concept. Therefore, the alpha-factor-based cellular communication and signal amplification system might be useful in applications that suffer from poor signal yield. Due to its modular design, the system could be applied in basically any cell-based biosensor or sensor-actor system. Immobilisation of the generated sensor and reporter cells in transparent natural polymers can be beneficial considering biosensor fabrication. Functionality of sensor and reporter cells in calcium-alginate beads or nano-printed arrays was successfully demonstrated. For the latter setup, fluorescence scanning and software-assisted fluorescence quantification was applied as a new detection method. In an experiment using an agarose-based two-compartment setup proposed by Jahn, 2011, properties of the alpha-factor-based cellular communication and signal amplification system after immobilisation were tested. These studies provide an initial experimental basis for an appropriate geometry of miniaturised immobilisation matrices with fluorescent yeast sensor and reporter cells in prospective biosensor designs.

Die vorliegende Dissertation beschreibt die Erarbeitung anwendbarer Methoden zum Aufbau Oberflächenplasmonenresonanz (SPR)-basierter DNA-Mikroarrays. Es werden die Beziehungen zwischen allen Teilschritten der Entwicklung eines DNA-Biosensors aufgezeigt. Die Sondendichte auf der Sensoroberfläche ist entscheidend für die Leistungsfähigkeit eines DNA-Chips. In dieser Arbeit werden thiolmodifizierte Sonden und solche mit Phosphorothioatgruppen verwendet und verglichen. Der Aufbau selbstorganisierender Monoschichten, bestehend aus Mercaptoalkoholen und thiolmodifizierten DNA-Einzelsträngen, wird mittels Röntgenphotoelektronenspektroskopie untersucht. Es werden bis zu 180 Spots auf einem SPR-Chip aufgetragen. Eine weitere Erhöhung der Anzahl an Sondenorten pro Chip wird mit einer hydrophil/hydrophoben Strukturierung der Arrayoberfläche erreicht. Dies erfolgt durch das Mikrokontaktdrucken mit Alkanthiolen. Die selektiven Hybridisierungen der Produkte der Polymerase-Kettenreaktion (PCR) werden bei SPR-Messungen auf DNA-Mikroarrays detektiert. Eine schnelle markierungsfreie Echtzeitanalyse wird bei Hybridisierungen im mikrofluidischen Kanal innerhalb weniger Minuten erzielt. Die Anwendbarkeit dieser Methoden wurde anhand der Mutationsanalyse der Fusionsgene AML1-ETO und CBFB-MYH11 bei der akuten myeloischen Leukämie bestätigt. Die Hybridisierungseffizienz auf DNA-Mikroarrays hängt stark von der Sodensequenz ab. SPR-Experimente zeigen, dass die Ausbildung der Haarnadelstrukturen die Ursache dafür ist. Ein Computerprogramm (EGNAS) auf Grundlage eines neu entwickelten Nucleobasen-Sequenzentwurf-Algorithmus, ermöglicht die Generierung vollständiger Sequenzsätze. Die Intra- und Interstrangeigenschaften dieser Sequenzen können kontrolliert werden, um Haarnadelstrukturen und Kreuzhybridisierungen zu vermeiden. Dadurch können optimierte Sequenzen für Anwendungen auf DNA-Chips oder in der DNA-Nanobiotechnologie entworfen werden.