Fluorescent labeling of biological materials using small organic dyes is widely employed in the life sciences and have been used in a variety of applications that include diagnostics and imaging. Quantum dots have the potential to overcome problems encountered by organic molecules and have been exploited for applications in biological imaging and in single particle tracking studies. The dithiolane ring can be exploited to attach a diversity of organic compounds to CdSe–ZnS core–shell nanoparticles. The introduction of spectroscopic labels as trans-azobenzene chromophores offers the opportunity to quantify the average number of dithiolane anchoring groups attached to each quantum dot. The transition from monomeric ligands with a single dithiolane anchor to polymeric ligands with multiple dithiolane anchoring groups can be exploited to raise the number of chromophoric labels adsorbed on each quantum dot. Systems showing FRET have been developed on the basis of supramolecular association of BODIPY based dyes or quantum dots as donors and organic chromophores as acceptors. Amino - terminated dyes and quantum dots associate with the chromophores through an ammonium moiety on addition of acid, thereby bringing them closer. Addition of base increases back the fluorescence intensity of the donor completely because of the dissociation. However a similar system with quantum dots as donor, show a very small restoration of fluorescence possibly due to non-specific interaction. In the next project, introduction of spectroscopic labels, in the form of BODIPY dye within the ligands offered the opportunity to quantify the average number of dithiolane anchoring groups attached to each quantum dot. Both fluorescence resonance energy transfer and electron transfer mechanisms are responsible for the quenching of quantum dot fluorescence and unfortunately does not make the system suitable for pH sensing. In the final project, BODIPY-oxazine based fluorophore – photochrome dyad has been assembled by a connecting triazole ring, such that the emission of the former can be modulated by the electronic and structural changes caused by the photoinduced transformations of the later. Further experiments need to be conducted on the fluorophore – photochrome dyads to switch the luminescence of the former with optical inputs.

Fluorescence-based assays have gained an ever-increasing popularity in life sciences. One of these rapidly emerging techniques is Protein Induced Fluorescence Enhancement (PIFE). Traditional explanations of PIFE focused exclusively on the role of the protein and largely neglected the role of the mediator DNA. In the same time, the existing models of PIFE were denying its exactly opposite effect. In the first part of the current dissertation we focus on a better understanding of PIFE, stimulated by the direct observation of its opposite effect, Induced Fluorescence Enhancement Quenching (PIFQ). This study offered us the leverage for obtaining on-demand fluorescence modulation in cyanine dyes. The following two chapters harvest this control over fluorescence modulation to generate two biotechnology applications: a sensitive potassium sensor with embedded fluorescent transducer, and a simple protocol for the fluorescent detection of His-tagged proteins. In the last part, a variety of fluorescence tools including Förster resonance energy transfer, fluorescence enhancement, and fluorescence quenching are employed for a much more complex task; to demystify the behavior of the human Maturation of Okazaki Fragments (MOF) machinery. First, we reconstituted the human MOF reaction and showed that it behaves considerably different than its well-established yeast homolog. Subsequently, our toolbox of fluorescence-based assays was used to pinpoint the kinetics and dynamics that lead to this unexpected MOF behavior.

Mit dem Ziel stabile und photomodulierbare Fluorophore für ihre direkte Anwendung in der hochaufgelösten Mikroskopie, wurde die Synthese und Charakterisierung von neuen fern Rot emittierender photoschaltbarer Fluorophore erreicht. Hierbei wurde die elektronische Kopplung zwischen den Komponenten tiefgreifend untersucht, und die Struktur Eigenschafts Beziehung etabliert. Durch die Wechselwirkung der photochromen Einheit mit dem Fluorophor, konnte die Fluoreszenzemission ein- und ausgeschaltet werden. Zusätzlich wurden Einkapselungs Experimente in Micellen durchgeführt, um die Wasserlöslichkeit der synthetisierten Verbindungen zu untersuchen. Letzlich, wurden mögliche Anwendungen mittels Fluoreszenzmikroskopie geprüft. Mit dem Ziel hochaufgelöste Bilder unter biologischen Bedingungen zu erhalten, wurde die Verkapselung der Dyaden in riesige unilamellare Vesikel erprobt. Unter Ausnutzung der Vorteile nichtlinearer Prozesse wurde die Synthese und Charakterisierung von photochromen Verbindungen, die in der Lage indirekt durch einen anfänglichen sensibilisierten Prozess geschaltet werden, untersucht. Zu diesem Zweck wurde ein Triarylamin Chromophor als Zwei-Photonenabsorber kovalent an einen Azobenzol verbunden. Die Charakterisierung der angeregten Zustandsdynamik wurde ausgeführt und die zwei Photonen induzierte Isomerisierung der Dyade bestätigt. Eine detaillierte Untersuchung der elektrochemischen Eigenschaften wurde durchgeführt und Richtlinien zur Verbesserung des Systems wurden kurz genannt. / With the purpose of designing stable and photomodulable fluorophores for their direct application in subdiffraction microscopy techniques, the synthesis and characterization of new far-red emitting photoswitchable fluorophores was accomplished. Fluorescence emission was efficiently modulated or switched On and Off by the interaction of the photochromic unit with the fluorescent-unit. Additionally, encapsulation experiments in micelles were performed to investigate the water solubility of the synthesized compounds. Finally, potential applications were examined with fluorescence microscopy, encapsulating the dyads in giant uni-lamellar vesicles under biological conditions to explore the feasibility to obtain highly resolved subdiffraction images. Exploiting the advantages of nonlinear processes, the synthesis and characterization of photochromes which are able to be switched indirectly through an initial sensitized event were studied. With this determination a two-photon absorbing triarylamine chromophore was covalently linked to an electron poor azobenzene. In-depth characterization of the excited state dynamics was performed and two photon induced isomerization of the dyad was confirmed. A detailed study of the electrochemical properties was set and guidelines towards the improvement of the system were succinctly mentioned.

Fluorescence imaging has been increasingly relied upon as the method of choice for many biological and medical applications. As demands for more sensitive and higher resolution imaging are ever-increasing, it is critical that photostable, and robust fluorophores capable of delivering high emission rates are available. Fluorescent silver nanoclusters offer an attractive compromise between the photostability and brightness of quantum dots and the compact versatility of organic chromophores. They have been shown to be superior in many roles, including as single molecule fluorophores and bulk multiphoton biological staining agents. The two-photon absorption cross sections are several orders of magnitude larger than commercially-available dyes, and they have demonstrated superior photostability under high intensity irradiation. In addition to the endogenous effects of the cluster, its small size of only a few atoms renders it highly susceptible to surface and environmental effects, which manifests, for example, in the observed photoinduced charge transfer between the silver cluster and oligonucleotide. This state has been shown to be highly advantageous in imaging applications, as control of this state enables better control over the time-averaged emission rate of the molecule. The mechanism of charge transfer, and the possible means by which this state can be controlled will be also be investigated in this work.