@phdthesis{Suetterlin2013, author = {S{\"u}tterlin, Martin}, title = {New inverse hydogel opals as protein responsive sensors}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70179}, school = {Universit{\"a}t Potsdam}, year = {2013}, abstract = {In this work, the development of temperature- and protein-responsive sensor materials based on biocompatible, inverse hydrogel opals (IHOs) is presented. With these materials, large biomolecules can be specifically recognised and the binding event visualised. The preparation of the IHOs was performed with a template process, for which monodisperse silica particles were vertically deposited onto glass slides as the first step. The obtained colloidal crystals with a thickness of 5 μm displayed opalescent reflections because of the uniform alignment of the colloids. As a second step, the template was embedded in a matrix consisting of biocompatible, thermoresponsive hydrogels. The comonomers were selected from the family of oligo(ethylene glycol)methacrylates. The monomer solution was injected into a polymerisation mould, which contained the colloidal crystals as a template. The space in-between the template particles was filled with the monomer solution and the hydrogel was cured via UV-polymerisation. The particles were chemically etched, which resulted in a porous inner structure. The uniform alignment of the pores and therefore the opalescent reflection were maintained, so these system were denoted as inverse hydrogel opals. A pore diameter of several hundred nanometres as well as interconnections between the pores should facilitate a diffusion of bigger (bio)molecules, which was always a challenge in the presented systems until now. The copolymer composition was chosen to result in a hydrogel collapse over 35 °C. All hydrogels showed pronounced swelling in water below the critical temperature. The incorporation of a reactive monomer with hydroxyl groups ensured a potential coupling group for the introduction of recognition units for analytes, e.g. proteins. As a test system, biotin as a recognition unit for avidin was coupled to the IHO via polymer-analogous Steglich esterification. The amount of accessible biotin was quantified with a colorimetric binding assay. When avidin was added to the biotinylated IHO, the wavelength of the opalescent reflection was significantly shifted and therefore the binding event was visualised. This effect is based on the change in swelling behaviour of the hydrogel after binding of the hydrophilic avidin, which is amplified by the thermoresponsive nature of the hydrogel. A swelling or shrinking of the pores induces a change in distance of the crystal planes, which are responsible for the colour of the reflection. With these findings, the possibility of creating sensor materials or additional biomolecules in the size range of avidin is given.}, language = {en} } @misc{RiedelsbergerDreyerGonzalez2015, author = {Riedelsberger, Janin and Dreyer, Ingo and Gonzalez, Wendy}, title = {Outward rectification of voltage-gated K+ channels evolved at least twice in life history}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {521}, issn = {1866-8372}, doi = {10.25932/publishup-40959}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409594}, pages = {17}, year = {2015}, abstract = {Voltage-gated potassium (K+) channels are present in all living systems. Despite high structural similarities in the transmembrane domains (TMD), this K+ channel type segregates into at least two main functional categories-hyperpolarization-activated, inward-rectifying (Kin) and depolarization-activated, outward-rectifying (Kout) channels. Voltage-gated K+ channels sense the membrane voltage via a voltage-sensing domain that is connected to the conduction pathway of the channel. It has been shown that the voltage-sensing mechanism is the same in Kin and Kout channels, but its performance results in opposite pore conformations. It is not known how the different coupling of voltage-sensor and pore is implemented. Here, we studied sequence and structural data of voltage-gated K+ channels from animals and plants with emphasis on the property of opposite rectification. We identified structural hotspots that alone allow already the distinction between Kin and Kout channels. Among them is a loop between TMD S5 and the pore that is very short in animal Kout, longer in plant and animal Kin and the longest in plant Kout channels. In combination with further structural and phylogenetic analyses this finding suggests that outward-rectification evolved twice and independently in the animal and plant kingdom.}, language = {en} } @phdthesis{Inal2013, author = {Inal, Sahika}, title = {Responsive polymers for optical sensing applications}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-70806}, school = {Universit{\"a}t Potsdam}, year = {2013}, abstract = {LCST-type synthetic thermoresponsive polymers can reversibly respond to certain stimuli in aqueous media with a massive change of their physical state. When fluorophores, that are sensitive to such changes, are incorporated into the polymeric structure, the response can be translated into a fluorescence signal. Based on this idea, this thesis presents sensing schemes which transduce the stimuli-induced variations in the solubility of polymer chains with covalently-bound fluorophores into a well-detectable fluorescence output. Benefiting from the principles of different photophysical phenomena, i.e. of fluorescence resonance energy transfer and solvatochromism, such fluorescent copolymers enabled monitoring of stimuli such as the solution temperature and ionic strength, but also of association/disassociation mechanisms with other macromolecules or of biochemical binding events through remarkable changes in their fluorescence properties. For instance, an aqueous ratiometric dual sensor for temperature and salts was developed, relying on the delicate supramolecular assembly of a thermoresponsive copolymer with a thiophene-based conjugated polyelectrolyte. Alternatively, by taking advantage of the sensitivity of solvatochromic fluorophores, an increase in solution temperature or the presence of analytes was signaled as an enhancement of the fluorescence intensity. A simultaneous use of the sensitivity of chains towards the temperature and a specific antibody allowed monitoring of more complex phenomena such as competitive binding of analytes. The use of different thermoresponsive polymers, namely poly(N-isopropylacrylamide) and poly(meth)acrylates bearing oligo(ethylene glycol) side chains, revealed that the responsive polymers differed widely in their ability to perform a particular sensing function. In order to address questions regarding the impact of the chemical structure of the host polymer on the sensing performance, the macromolecular assembly behavior below and above the phase transition temperature was evaluated by a combination of fluorescence and light scattering methods. It was found that although the temperature-triggered changes in the macroscopic absorption characteristics were similar for these polymers, properties such as the degree of hydration or the extent of interchain aggregations differed substantially. Therefore, in addition to the demonstration of strategies for fluorescence-based sensing with thermoresponsive polymers, this work highlights the role of the chemical structure of the two popular thermoresponsive polymers on the fluorescence response. The results are fundamentally important for the rational choice of polymeric materials for a specific sensing strategy.}, language = {en} } @phdthesis{Heinsohn2022, author = {Heinsohn, Natascha}, title = {Development of a fiber-based sensor for the molecular detection of pathogens using Legionella as an example}, doi = {10.25932/publishup-56683}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-566833}, school = {Universit{\"a}t Potsdam}, pages = {X, 175}, year = {2022}, abstract = {Fiber-based microfluidics has undergone many innovative developments in recent years, with exciting examples of portable, cost-effective and easy-to-use detection systems already being used in diagnostic and analytical applications. In water samples, Legionella are a serious risk as human pathogens. Infection occurs through inhalation of aerosols containing Legionella cells and can cause severe pneumonia and may even be fatal. In case of Legionella contamination of water-bearing systems or Legionella infection, it is essential to find the source of the contamination as quickly as possible to prevent further infections. In drinking, industrial and wastewater monitoring, the culture-based method is still the most commonly used technique to detect Legionella contamination. In order to improve the laboratory-dependent determination, the long analysis times of 10-14 days as well as the inaccuracy of the measured values in colony forming units (CFU), new innovative ideas are needed. In all areas of application, for example in public, commercial or private facilities, rapid and precise analysis is required, ideally on site. In this PhD thesis, all necessary single steps for a rapid DNA-based detection of Legionella were developed and characterized on a fiber-based miniaturized platform. In the first step, a fast, simple and device-independent chemical lysis of the bacteria and extraction of genomic DNA was established. Subsequently, different materials were investigated with respect to their non-specific DNA retention. Glass fiber filters proved to be particularly suitable, as they allow recovery of the DNA sample from the fiber material in combination with dedicated buffers and exhibit low autofluorescence, which was important for fluorescence-based readout. A fiber-based electrophoresis unit was developed to migrate different oligonucleotides within a fiber matrix by application of an electric field. A particular advantage over lateral flow assays is the targeted movement, even after the fiber is saturated with liquid. For this purpose, the entire process of fiber selection, fiber chip patterning, combination with printed electrodes, and testing of retention and migration of different DNA samples (single-stranded, double-stranded and genomic DNA) was performed. DNA could be pulled across the fiber chip in an electric field of 24 V/cm within 5 minutes, remained intact and could be used for subsequent detection assays e.g., polymerase chain reaction (PCR) or fluorescence in situ hybridization (FISH). Fiber electrophoresis could also be used to separate DNA from other components e.g., proteins or cell lysates or to pull DNA through multiple layers of the glass microfiber. In this way, different fragments experienced a moderate, size-dependent separation. Furthermore, this arrangement offers the possibility that different detection reactions could take place in different layers at a later time. Electric current and potential measurements were collected to investigate the local distribution of the sample during migration. While an increase in current signal at high concentrations indicated the presence of DNA samples, initial experiments with methylene blue stained DNA showed a temporal sequence of signals, indicating sample migration along the chip. For the specific detection of a Legionella DNA, a FISH-based detection with a molecular beacon probe was tested on the glass microfiber. A specific region within the 16S rRNA gene of Legionella spp. served as a target. For this detection, suitable reaction conditions and a readout unit had to be set up first. Subsequently, the sensitivity of the probe was tested with the reverse complementary target sequence and the specificity with several DNA fragments that differed from the target sequence. Compared to other DNA sequences of similar length also found in Legionella pneumophila, only the target DNA was specifically detected on the glass microfiber. If a single base exchange is present or if two bases are changed, the probe can no longer distinguish between the DNA targets and non-targets. An analysis with this specificity can be achieved with other methods such as melting point determination, as was also briefly indicated here. The molecular beacon probe could be dried on the glass microfiber and stored at room temperature for more than three months, after which it was still capable of detecting the target sequence. Finally, the feasibility of fiber-based FISH detection for genomic Legionella DNA was tested. Without further processing, the probe was unable to detect its target sequence in the complex genomic DNA. However, after selecting and application of appropriate restriction enzymes, specific detection of Legionella DNA against other aquatic pathogens with similar fragment patterns as Acinetobacter haemolyticus was possible.}, language = {en} }