Design, synthesis and application of ultrastable rylene dyes for fluorescent labeling of biomolecules

Studies of organic fluorescent dyes are experiencing a renaissance related to the increasing demands posed by new microscopy techniques for high resolution and high sensitivity. While in the last decade single molecule equipment and methodology has significantly advanced and in some cases reached theoretical limits (e.g. detectors approaching unity quantum yields) unstable emission from chromophores and photobleaching become more and more the bottleneck of the advancement and spreading of single-molecule fluorescence studies. The main goal of this work was the synthesis of fluorophores that are water-soluble, highly fluorescent in an aqueous environment, have a reactive group for attachment to a biomolecule and posses exceptional photostability. An approach towards highly fluorescent, water-soluble and monofunctional perylene-3,4,9,10-tetracarboxdiimide and terrylene-3,4:11,12-tetra carboxidiimide chromophores was presented. A new synthetic strategy for the desymmetrization of perylenetetracarboximides was elaborated; water-solubility was accomplished by introducing sulfonyl substituents in the phenoxy ring. Two strategies have been followed relying on either non-specific or site specific labeling. For this purpose a series of new water-soluble monofunctional perylene and terrylene dyes, bearing amine or carboxy group were prepared. The reactivity and photophysical properties of these new chromophores were studied in aqueous medium. The most suitable chromophores were further derivatized with amine or thiol reactive groups, suitable for chemical modification of proteins. The performance of the new fluorescent probes was assessed by single molecule enzyme tracking, in this case phospholipase acting on phospholipid supported layers. Phospholipase-1 (PLA-1) was labeled with N-hydroxysuccinimide ester functionalized perylene and terrylene derivatives. The purification of the conjugates was accomplished by novel convenient procedure for the removal of unreacted dye from labeled enzymes, which involves capturing excess dye with a solid support. This novel strategy for purification of bioconjugates allows convenient and fast separation of labeled proteins without the need for performing time consuming chromatographic or electrophoretic purification steps. The outstanding photostability of the dyes and, associated therewith, the extended survival times under strong illumination conditions allow a complete characterization of enzyme action on its natural substrates and even connecting enzyme mobility to catalytic activity. For site-specific attachment of the rylene dyes to proteins the chromophores were functionalized with thioesters or nitrilotriacetic acid groups. This allowed attachment of the emitters to the N-terminus of proteins by native chemical ligation or complexation with His-tagged polypeptides at the N- or C-termini, respectively. The synthesis of a water-soluble perylenebis (dicarboximide) functionalized with a thioester group was presented. This chromophore exhibits an exceptional photostability and a functional unit for site-specific labeling of proteins. The suitability of the fluorophore as a covalent label was demonstrated via native chemical ligation with protein containing N-terminal cystein residue. We exploited also oligohisitidine sequences as recognition elements for site-selective labeling. The synthesis of a new water-soluble perylene chromophore, containing a nitrilotriacetic acid functional group was demonstrated, using solution-phase and solid-phase approaches. This chromophore combines the exceptional photophysical properties of the rylene dyes and a recognition unit for site-specific labeling of proteins. An important feature of the label is the unchanged emission of the dye upon complexation with nickel ions.

Fluorescent ionene-dye nanoparticles by electrostatic self-assembly

It is investigated that the association of linear cationic model polyelectrolytes with oppositely charged pyrenetetrasulfonate (PY) in aqueous solution. For this purpose water soluble ionenes were prepared via Menschutkin reaction from 1-4-diazabicyclo [2.2.2] octane and e.g. 1,6-dibromohexane and 1,4 dibromotransbuten. The complex formation between dye molecules PY and oppositely charged ionenes (PD4, PD6, PD4-2 and PD4coPD6) of different chemical structures in aqueous solution was studied by light scattering (LS), small angle neutron scattering (SANS), UV-Vis, fluorescence spectroscopy and atomic force microscopy (AFM). Spectrophotometric titration results revealed that PY molecules were bind to ionenes cooperative process due to π-π interaction. Cooperative binding constant KD was determined as 6.4 x 10^6 M^-1 (+ or - 10^5 M^-1). It was found that binding mode and geometry of PY is predominantly depending on inter-charge distances of corresponding ionenes. Resultant complexes have exhibited size and structure variation as a function of charge ratio (L), ionic strength, inter-charge distances. Spherical dye-ionene complexes of which radius of gyration ranging between (RG) 50 and 190 nm have been observed in PD4-PY system while this was not possible with a different ionene (PD6) or either case ionene excess. It was found that most of the PD4-PY complexes had RG / RH ~ 0.78. Based on the AFM and LS results, spherical complexes have certain colloidal stability and their size can effectively controlled by changing the L.

Alpha, Omega end group functionalization of RAFT polymers based on pentafluorophenyl esters and methane thiosulfonates

While polymers with different functional groups along the backbone have intensively been investigated, there is still a challenge in orthogonal functionalization of the end groups. Such well-defined systems are interesting for the preparation of multiblock (co) polymers or polymer networks, for bio-conjugation or as model systems for examining the end group separation of isolated polymer chains. rnHere, Reversible Addition Fragmentation Chain Transfer (RAFT) polymerization was employed as method to investigate improved techniques for an a, w end group functionalization. RAFT produces polymers terminated in an R group and a dithioester-Z group, where R and Z stem from a suitable chain transfer agent (CTA). rnFor alpha end group functionalization, a CTA with an activated pentafluorophenyl (PFP) ester R group was designed and used for the polymerization of various methacrylate monomers, N-isopropylacrylamide and styrene yielding polymers with a PFP ester as a end group. This allowed the introduction of inert propyl amides, of light responsive diazo compounds, of the dyes NBD, Texas Red, or Oregon Green, of the hormone thyroxin and allowed the formation of multiblocks or peptide conjugates. rnFor w end group functionalization, problems of other techniques were overcome through an aminolysis of the dithioester in the presence of a functional methane thiosulfonate (MTS), yielding functional disulfides. These disulfides were stable under ambient conditions and could be cleaved on demand. Using MTS chemistry, terminal methyl disulfides (enabling self-assembly on planar gold surfaces and ligand substitution on gold and semiconductor nanoparticles), butynyl disulfide end groups (allowing the “clicking” of the polymers onto azide functionalized surfaces and the selective removal through reduction), the bio-target biotin, and the fluorescent dye Texas Red were introduced into polymers. rnThe alpha PFP amidation could be performed under mild conditions, without substantial loss of DTE. This way, a step-wise synthesis produced polymers with two functional end groups in very high yields. rnAs examples, polymers with an anchor group for both gold nanoparticles (AuNP) and CdSe / ZnS semi-conductor nanoparticles (QD) and with a fluorescent dye end group were synthesized. They allowed a NP decoration and enabled an energy transfer from QD to dye or from dye to AuNP. Water-soluble polymers were prepared with two different bio-target end groups, each capable of selectively recognizing and binding a certain protein. The immobilization of protein-polymer-protein layers on planar gold surfaces was monitored by surface plasmon resonance.Introducing two different fluorescent dye end groups enabled an energy transfer between the end groups of isolated polymer chains and created the possibility to monitor the behavior of single polymer chains during a chain collapse. rnThe versatility of the synthetic technique is very promising for applications beyond this work.

Glukose-konjugierte Hemmstoffe als Strategie der gezielten Hemmung des DNA-Reparaturproteins O 6 -Methylguanin-DNA-Methyltransferase in Tumorzellen und der Einfluss von ATP-binding cassette Transportern

Das DNA-Reparaturprotein O6-Methylguanin-DNA-Methyltransferase [MGMT] ist der Hauptresistenzfaktor gegenüber der zytotoxischen Wirkung von SN1-alkylierenden Zytostatika in der Tumortherapie. Die Verwendung der MGMT-Hemmstoffe O6-Benzylguanin [O6BG] und O6-(4-Bromothenyl)guanin [O6BTG] führte zu einer Sensibilisierung des Normalgewebes, was eine Dosis-Reduktion der Zytostatika erforderlich machte und die erhoffte Therapieverbesserung verhinderte. Aus diesem Grund ist eine Strategie der selektiven Hemmung des MGMT-Proteins (Targeting-Strategie) erforderlich, um die systemische Toxizität in der Kombinationsbehandlung zu reduzieren. In dieser Arbeit wurde die Anwendbarkeit der Glukose-Konjugation als Targeting-Strategie untersucht, da Tumorzellen einen erhöhten Glukoseverbrauch aufweisen und demzufolge Glukosetransporter überexprimieren. Die Glukose-Konjugate O6BG-Glu und O6BTG-Glu inhibierten MGMT in Tumorzellen und sensibilisierten die Zellen gegenüber den alkylierenden Agenzien Temozolomid [TMZ] und Lomustin [CCNU]. Des Weiteren inaktivierten die Glukose-Konjugate die MGMT-Aktivität im Tumor eines Xenograft-Mausmodells und reduzierten das Tumorwachstum nach einer TMZ-Behandlung im gleichen Ausmass wie die Inhibitoren O6BG und O6BTG. Trotzdem war auch mit den Glukose-Konjugaten keine Steigerung der Zytostatika-Dosis im Mausmodell möglich. Die Untersuchungen der Aufnahme von O6BG-Glu und O6BTG-Glu wiederlegten eine Involvierung der Glukosetransporter. Der Einsatz von spezifischen Glukosetransporter-Inhibitoren und Kompetitions-Experimenten führte zu keiner Verminderung der MGMT-Hemmung oder Aufnahme vom radioaktiven H3-O6BTG-Glu in die Zelle. Dies legt nahe, dass die Glukose-Konjugate über einen unspezifischen Mechanismus (aktiv) in die Zellen gelangen. Der Grund für eine mögliche unselektive Aufnahme könnte im hydrophoben Alkyllinker, der für die Konjugation des Glukosemoleküls verwendet wurde, begründet sein. Dies führt zur Generierung von amphipathischen Konjugaten, die eine initiale Bindung an die Plasmamembran aufweisen und eine Aufnahme über den Flip-Flop-Mechanismus (transbilayer transport) wahrscheinlich machen. Die amphipathische Molekülstruktur der Glukose-Konjugate führte zu einer Partikelbildung in wässrigen Lösungen, die eine Reduktion der Menge an aktiven Monomeren von O6BG-Glu und O6BTG-Glu bewirken, die zur Hemmung von MGMT zur Verfügung stehen. Der zweite Teil der Arbeit befasste sich mit der Rolle von ABC-Transportern hinsichtlich einer Targeting-Strategie von MGMT-Hemmstoffen. Obwohl eine hohe Expression dieser ABC-Transporter in Tumoren zur Resistenzentwicklung gegenüber Zytostatika führt, wurde ihr Einfluss auf MGMT-Hemmstoffe oder einer MGMT-Targeting-Strategie niemals untersucht. In dieser Arbeit wurde zum ersten Mal ein aktiver Efflux von MGMT-Hemmstoffen durch ABC-Transporter nachgewiesen. Die Inhibition von ABC-Transportern bewirkte eine schnellere Inaktivierung von MGMT durch die Glukose-Konjugate. Des Weiteren zeigten Kompetitions-Experimente mit den MGMT-Hemmstoffen eine verminderte Efflux-Rate von Fluoreszenzfarbstoffen, die spezifisch von ABC-Transportern exportiert werden. ABC-Transporter reduzieren die wirksame Konzentration des Hemmstoffes in der Zelle und beeinträchtigen somit die Effektivität der MGMT-Inhibition. Eine simultane Hemmung der ABC-Transporter P-glycoprotein (P-gp), multi resistance protein 1 (MRP1) and breast cancer resistance protein (BCRP) erhöhte die Effektivität der MGMT-Hemmstoffe (O6BG, O6BTG, O6BG-Glu, O6BTG-Glu) und verstärkte auf diese Weise die TMZ-induzierte Toxizität in Tumorzelllinien. Die Involvierung von ABC-Transportern in der intrazellulären Speicherung von MGMT-Hemmstoffen ist wahrscheinlich die Ursache für die beobachteten Unterschiede in der Sensibilisierung verschiedener Tumorzelllinien gegenüber Zytostatika durch das Glukose-Konjugat O6BG-Glu. Eine Strategie, den Einfluss von ABC-Transportern zu reduzieren und zukünftliche MGMT-Targeting-Strategien effizienter umzusetzen, ist die Verwendung von O6BTG als Ausgangssubstanz. Die höhere Inhibitionsfähigkeit der Bromthiophenmoleküle vermindert die erforderliche intrazelluläre Konzentration für eine vollständige MGMT-Hemmung und reduziert auf diese Weise den Einfluss von ABC-Transportern.

First contact imaging of nanoparticular siRNA – From synthesis to application of a prodye concept

Delivery of therapeutic nucleic acid based drugs is still very demanding and difficult to manage and monitor. For this reason, a precise method for the monitoring of RNAi pathways is necessary. This thesis explores a new approach for sensing of potentially therapeutic nucleic acids, using the interaction of so called prodyes with intracellular enzymes in a prodrug manner. To realize this concept, some non-fluorescent, fluorescein based asymmetric dyes were synthesized and their spectroscopic characteristics were studied. Azide-alkyne Click chemistry was applied for conjugation purposes, using a new protocol at weak acidic pH to get intact prodye constructs. Both, an electrophoretic mobility shift assay with polyacrylamide gels and in-cuvette experiments showed remarkable OFF-to-ON behavior of these new siRNA constructs under physiological conditions. After salt-free purification, subsequent hybridization to double-stranded ribonucleic acids and nanoformulation to lipoplexes, the prodye conjugated siRNA was examined in cellular uptake studies for First Contact Imaging. The investigated siRNA-prodye conjugates showed strong sensitivity to esterases, being hydrolyzed at the biolabile function and developing a strong fluorescence which was verified in bulk. As an optimization, a new profluorescent molecule system was designed and synthesized, which has a carbonate as biolabile 6’ protecting group and a highly water soluble 3’ clickable linker. This new non-fluorescent but colored prodye showed 12 - 320 times increased fluorescence intensities between OFF- and ON- states, depending to the deprotection method. This is the first reported molecule model of an asymmetric profluorescent fluorescein, having the very favorable 3’ & 6’ functions.