Homogene Immunoassays sind immunologische Testverfahren, bei deren Durchführung vollständig auf Separations- und Waschschritte verzichtet werden kann. Der Substrate Channeling Immunoassay beruht auf der Weitergabe eines Substrates in einem immunologischen Komplex aus zwei Enzymen. Das Produkt des ersten Enzyms dient dem zweiten Enzym als Substrat zur Generierung eines photometrisch nachweisbaren Produktes. Voraussetzung für diese Weitergabe ist die enge räumliche Nähe beider Enzyme. Diese Nähe wird durch eine Bindung zwischen Analyt und anti-Analyt Antikörper vermittelt. Ein solcher Substrate Channeling Immunoassay wurde unter Verwendung der Enzyme Glucoseoxidase und Peroxidase aufgebaut. Das so etablierte System war funktionstüchtig, jedoch blieb seine Sensitivität hinter der normaler, heterogener Immunoassays zurück. Die Grundlage eines Fluorescence Quenching Immunoassays ist der gegenseitige Ausschluß zweier Antikörper bei der Bindung eines Dihapten-Konjugates. Das Konjugat besteht dabei aus dem Analyten und einem Fluorophor. Die beiden um die Konjugatbindung konkurrierenden Antikörper sind ein anti-Analyt Antikörper und ein anti-Fluorophor Antikörper, der zudem über die Eigenschaft verfügt, bei Bindung des Fluorophors dessen Fluoreszenz zu löschen. Externe Gaben des freien Analyten verschieben das eingestellte Gleichgewicht in Richtung Fluorophor-Bindung und damit Fluoreszenz-Löschung. Die Änderung der Fluoreszenz ist direkt an die Konzentration des freien Analyten gekoppelt und dient zu deren Bestimmung. Ein solcher Fluorescence Quenching Immunoassays wurde für die Konzentrationsbestimmung des Herbizides Diuron etabliert. Die erreichten Sensitivitäten erlauben die praktische, immundiagnostische Anwendung des Systems. Ein Dihapten-Konjugat wurde ebenfalls zum Aufbau eines Verfahrens zur Selektion Antikörper produzierender Zellen eingesetzt. Die Selektion der Antikörper produzierenden Zellen erfolgt unter Verwendung eines Toxinkonjugates. Dieses Konjugat besteht aus einem Liganden und einem Toxin. Die Antikörperbindung des Liganden behindert sterisch die Wechselwirkung der Toxinkomponente im Konjugat mit deren Zielstruktur in oder auf der Zelle. Nur Zellen die einen geeigneten Antikörper sezernieren, überleben die Selektion und reichern sich in der Kultur an. Das Selektionsverfahren wurde erfolgreich für die Selektion von E.coli Zellen eingesetzt, die einen rekombinanten, Fluorescein bindenden Antikörper produzierten. Das hierfür synthetisierte Toxinkonjugat bestand aus Fluorescein (Ligand) und Ampicillin (Toxinkomponente). Eine Ablösung der bisher für diese Aufgabe gebräuchlichen, außerordentlich kostenintensiven, Screening Methoden wird damit möglich. / Homogeneous immunoassays are test systems which do not depend on separation steps. The substrate channeling immunoassay is based on the product/substrate transfer in an immunological complex built up by two enzymes. The product of the first enzyme functions as substrate for the second enzyme. The second enzyme generates a photometrically detectable product. The close proximity of these two enzymes is the basis of the substrate channeling. This proximity is created by antibody binding to the corresponding analyte. The enzymes glucose oxidase and peroxidase were used for the development of such an assay system. The established homogeneous immunoassay was functional. But the sensitivity of the assay was much lower than that of conventional heterogeneous immunoassays. The principle of a fluorescence quenching immunoassay is based on the fact that two antibodies exclude each other from binding to a dihapten conjugate. The conjugate consists of the analyte and the fluorophore. The two antibodies which compete for the conjugate binding are an anti-analyte antibody and an anti-fluorophore antibody. This anti-fluorophore antibody quenches the fluorescence of the fluorophore after binding. The addition of free analyte alters the equilibrium of the system so that the anti-fluorophore antibody is bound to the fluorophore and the fluorescence is quenched. The change in fluorescence is therefore an indicator of the concentration of free analyte added. A homogeneous fluorescence quenching immunoassay was established for the determination of the herbicide diuron. The sensitivities obtained allow the practical immunodiagnostic application of the system. A dihapten conjugate was also employed for the development of a selection method for antibody-producing cells. Toxin conjugates were used in this system. Each conjugate consisted of a ligand and a toxin. Antibody binding to the ligand sterically inhibits the toxin component to interact with its target structure. Only cells secreting a binding antibody will survive the selection and will accumulate in culture. The system was applied to the selection of E.coli cells producing a recombinant fluorescein-binding antibody. The toxin conjugate used in experiment consisted of fluorescein (ligand) and ampicillin (toxin component). This selection procedure allowed the isolation of recombinant antibody-producing E.coli cells. It has the potential to replace the time-consuming and labour-intensive methods used so far.

Photocontrol, the use of light-sensitive proteins to control events within living tissue, allows complex processes in higher organisms to be studied. The Halorhodospira halophila photoactive yellow protein (PYP) can be used to regulate transcription factor activity with blue light. Before any PYP-based system can probe complex processes in higher organisms, proof of functional expression in vivo is required. We linked d25 PYP to the C-terminus of blue fluorescent protein (BFP) and expressed variants of the fusion protein (BFPd25PYP) in E. coli and human embryonic kidney (HEK293) cells. Expression of BFPd25PYP in E. coli verified in vitro photoswitching. The fusion protein was successfully expressed in HEK293. Fluorescence studies of intact cells indicated chromophore uptake and incorporation into PYP in HEK293, while photoswitching of PYP was measured in protein isolated from HEK293. These findings are promising for the development of applications using PYP for in vivo mammalian photocontrol of biological events.

Photocontrol, the use of light-sensitive proteins to control events within living tissue, allows complex processes in higher organisms to be studied. The Halorhodospira halophila photoactive yellow protein (PYP) can be used to regulate transcription factor activity with blue light. Before any PYP-based system can probe complex processes in higher organisms, proof of functional expression in vivo is required. We linked d25 PYP to the C-terminus of blue fluorescent protein (BFP) and expressed variants of the fusion protein (BFPd25PYP) in E. coli and human embryonic kidney (HEK293) cells. Expression of BFPd25PYP in E. coli verified in vitro photoswitching. The fusion protein was successfully expressed in HEK293. Fluorescence studies of intact cells indicated chromophore uptake and incorporation into PYP in HEK293, while photoswitching of PYP was measured in protein isolated from HEK293. These findings are promising for the development of applications using PYP for in vivo mammalian photocontrol of biological events.

Three different types of cage crown ethers have been prepared and their complexation properties with Ag(I) have been studied. Atomic absorption, fluorescence quenching, and UV absorption have been used to study the interaction between the hosts (cage crown ethers) and guests (Ag+). For the cage-annulated crown ethers that contain aromatic rings, cation-π and π-π interactions may contribute significantly to the overall complexation ability of the host system. Piperazine groups may cooperate, and the piperazine nitrogen atoms provide unshared electrons, which may form a complex with Ag+. In addition, relatively soft donor atoms (e.g., Br) are well-suited for complexation with Ag+, which is a softer Lewis acid than alkali metal cations.

Small molecule walkers developed to date take advantage of the reversibility of dynamic covalent bond formation to transport molecular fragments along molecular tracks using both diffusion processes and ratchet mechanisms. However, external intervention (the addition of chemical reagents and/or irradiation with light) is required to mediate each step taken by the walker unit in systems reported so far. In this Thesis, the first synthetic small molecule able to walk back-and-forth upon an oligoethylenimine track without external intervention via intramolecular Michael and retro- Michael reactions is described. The 1D random walk is highly processive and exchange takes place between adjacent amine groups in a stepwise fashion. The walker is used to perform a simple task: quenching of the fluorescence of an anthracene group situated at one end of the track as a result of the walking progress. In the presence of excess of base, the molecule preferentially ‘walks’ towards the favoured final foothold of tracks of increasing length and it is possible to monitor the population of all or a few positional isomers over time. In each case the molar fraction of walkers reaching the final foothold is determined quantitatively by 1H NMR. Control over the rate of exchange is achieved by varying the amount of base added. The dynamic migration of a small molecule upon the track is a diffusion process limited to one dimension and as such can in principle be described using the one dimensional random walk. Chapter I identifies a set of fundamental walker characteristics and includes an overview of the DNA-based and small molecule transporting systems published to date. Chapter II describes the inspiration for this work and model studies which lay the groundwork for the research presented in this thesis. The initial track architecture and optimisation of reaction conditions are demonstrated using a simple model compound which then led to the development and a detailed investigation of a first synthetic small molecule able to walk upon an oligoethylenimine track without external intervention. Chapter III presents a modified synthetic route towards the desired walker-track architectures and a comprehensive investigation of the dynamic properties of a series of tracks of increasing length upon which the walker migrates in a unidirectional fashion. The Outlook contains closing remarks about the scope and significance of the presented work as well as ideas for the design of novel small-molecule walkers, some of which are well under way in the laboratory. Chapter II (with the exception of model studies included at the beginning of the chapter) is presented in the form of article that has recently been published. No attempt has been made to re-write this work out of context other than merging content of the article with the supplementary information published together with the article. Chapter II is reproduced in the Appendix in its published format.

The primary goals of our research are to understand the virology and enzymology of human T-cell leukemia virus type I (HTLV-I) that will lead to the development of treatments for patients infected with HTLV-I. HTLV-I is an oncogenic virus of the Retroviridae family and is the causative agent of adult T-cell leukemia/lymphoma (ATL), tropical spastic paraparesis/HTLV-I associated myelopathy (TSP/HAM). HTLV-I has been classified as a dangerous emerging pathogen by the Centers for Disease Control and Prevention with at least 20 million people infected with the virus. This is a significant problem because there are currently no effective treatments to control HTLV-I infection and prevent or treat HTLV-I induced ATL and TSP/HAM. The protease is necessary for retroviral maturation and replication and is, therefore, an attractive target for inhibitor design. Investigation of peptide mimetic compounds incorporating the tetrahedral intermediate of aspartyl protease catalyzed cleavage are crucial for the development of lead inhibitors. Compounds containing statine, 4-amino-3-hydroxy-5-phenylpentanoic acid (AHPPA), or hydroxyethylamine (HEA) are presented in this work. The best compound was a statine-based inhibitor, which had a Ki = 29 +/- 4 nM and 88% inhibition against an HTLV-I protease native substrate in a FRET assay.

Les matrices d’excitation et d’émission de fluorescence (MEEF) sont utilisées pour caractériser la matière organique naturelle (MON). Afin de mieux exploiter ces informations, un algorithme trilinéaire, PARAFAC, est employé. Après l’élimination des diffusions Rayleigh et Raman et la correction de l’effet d’écran, cette méthode permet de séparer les composants spectraux présents dans les MEEF.Ce travail présente deux études : la qualification et la quantification de la MON selon son origine environnementale et le calcul des constantes de complexation de la MON et du cuivre sous forme ionique.Les composants spectraux et leurs intensités relatives sont calculés par PARAFAC à partir 1146 échantillons regroupés suivant les missions, leur type de milieu, ou le niveau de salinité. Pour étudier ces composants, une nouvelle représentation spectrale est proposée afin de mettre en évidence leur variabilité spectrale. Les résultats montrent que le regroupement d’échantillons d’origine diverse conserve le recouvrement spectral global et les intensités relatives. Sur l’ensemble du domaine spectral, les zones correspondant aux substances humiques sont peu variables, comparées à la zone protéinique.La complexation des métaux par la MON est analysée par une technique combinant quatre outils : l’ajout logarithmique d’ions métalliques, la mesure de MEEF, la méthode PARAFAC et l’algorithme PROSECE. La mesure du quenching de fluorescence ne se limite pas seulement à la modélisation d’une intensité de fluorescence mais à celle de l’intensité relative de chaque composant PARAFAC surpassant ainsi les méthodes utilisées jusqu’à présent. Finalement, l’application de cette technique originale permet de quantifier les propriétés de complexation de la MON à l'aide d'un modèle de complexation utilisant 2 sites de complexation par composant en utilisant la totalité du signal de fluorescence. / Fluorescence excitation and emission matrices (EEM) are used to characterize natural organic matter (NOM). To make best use of this information, PARAFAC, a trilinear algorithm is employed. After removing Rayleigh and Raman scattering and correction of the inner filter effect, this method allows separating the spectral components present in MEEF.This work presents two studies: the characterization and quantification of NOM according to its origin and calculation of environmental complexation constants of NOM towards copper as ionic form.Spectral components and their relative intensities are calculated by PARAFAC from 1146 samples gathered according to the missions, the medium type, or the salinity level. To study these components, a new spectral representation is proposed in order to highlight their spectral variability. The results show that even when samples spectra of various origins are clustered, the overall spectral overlap and the relative intensities remain almost similar. On the whole spectral range, areas corresponding to humic substances are quite variable, compared to the protein zone.Metal complexation by NOM is analyzed by combination of four tools: metal ions logarithmic addition, MEEF measurement, the PARAFAC dissociation method and the PROSECE modelling algorithm. Fluorescence quenching measurement is not only limited to the modelling of fluorescence intensity but also to the relative intensity of each PARAFAC-dissociated component though surpassing the methods used so far. Finally, the application of this improving technique leads to quantify NOM complexation properties using a two-complexing sites complexation model for each PARAFAC-dissociated component by using the whole fluorescence signal.

This diploma thesis was focused on studying the interaction of humic substances with ionic organic xenobiotics and its structural aspects. The method was chosen from my bachelor thesis, steady-state fluorescence spectroscopy, which is suitable for substances with weak fluorescence. The results showed that the interaction between humic acids and representatives of ionic organic xenobiotics (Septonex) was reflected in fluorescence quenching of humic acids and the shift of emission maximum to lower wavelength, hypsochromic (blue) shift. From the measurement results, we can assume that the interaction that is formed between the aromatic structures in humic acids and Septonex could be -cation interaction.

In this study, we synthesized small-molecule, water-soluble, fluorescein-containing ureido compounds 6 and 8 as target receptors for cytosine free bases and then investigated the binding of cytosine free bases with the receptors using 15N NMR spectroscopy and partially labeled cytosine-2,4-13C-1,3,4-15N-cytosine. Binding with the receptor 6a (the disodium form of 6) caused the chemical shift of the nitrogen atom of the amino group of cytosine to move downfield; binding of the receptor 8a (the disodium form of 8), which is possessing no corresponding aryl nitrogen atom, had no effect on this signal. Fluorescence spectroscopy revealed that binding of cytosine and its derivatives led to quenching of the fluorescence of receptor 6a; in contrast, the quenching of receptor 8a was only slightly affected by cytosine. Because the fluorescence of 6a was not quenched by either deoxycytidine or uracil, it appears that this receptor is a specific for cytosine among the DNA bases. We used the fluorescence of 6a to measure the apparent binding constants for various cytosine derivatives, including the anticancer prodrug 5-fluorocytosine. Receptor 6a is the first small-molecule, water-soluble fluorescent receptor for the specific binding of cytosine free bases in aqueous solution.

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