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Efficient quadrupolar chromophores (A–pi–A) with triarylborane moieties as acceptors have been studied by the Marder group regarding their non‐linear optical properties and two‐photon absorption ability for many years. Within the present work, this class of dyes found applications in live‐cell imaging. Therefore, the dyes need to be water‐soluble and water‐stable in diluted aqueous solutions, which was examined in Chapter 2. Furthermore, the influence of the pi‐bridge on absorption and emission maxima, fluorescence quantum yields and especially the two-photon absorption properties of the chromophores was investigated in Chapter 3. In Chapter 4, a different strategy for the design of efficient two‐photon excited fluorescence imaging dyes was explored using dipoles (D–A) and octupoles (DA3). Finding the optimum balance between water‐stability and pi‐conjugation and, therefore, red‐shifted absorption and emission and high fluorescence quantum yields, was investigated in Chapter 5
In dieser Arbeit ist die Synthese von funktionalisiertem Nanodiamant mit bioaktiven Substanzen, welche vor allem als Wirkstofftransporter eingesetzt werden sollen, beschrieben. Dazu werden zum einen bereits bekannte Anbindungsmöglichkeiten an Nanodiamant, wie zum Beispiel die Klick-Reaktion, sowie die Ausbildung von Amidbrücken verwendet. Zum anderen werden neuartige Funktionalisierungsmöglichkeiten wie Protein Ligation und Thioharnstoffbrücken verwendet und somit das Repertoire an bekannten Anbindungsreaktion erweitert.
Des weiteren wurde ein multifunktionales Nanodiamantsystem synthetisiert. Dieses ist in der Lage, zwei verschiedene Moleküle auf einem Partikel zu immobilisieren. Die verwendeten Methoden ermöglichen die Anbindung verschiedener Substanzen aus unterschiedlichen Molekülgruppen an Nanodiamanten und sind somit universell einsetzbar.
Pyrene is a polycyclic aromatic hydrocarbon (PAH) that has very interesting photophysical properties which make it suitable for a broad range of applications. The 2,7-positions of pyrene are situated on nodal planes in both the HOMO and LUMO. Hence, electrophilic reactions take place at the 1-, 3-, 6-, and 8-positions. The goal of this project was to develop novel pyrene derivatives substituted at the 2- and 2,7-positions, with very strong donors or/and acceptors, to achieve unprecedented properties and to provide a deeper understanding of how to control the excited states and redox properties. For that reason, a julolidine-type moiety was chosen as a very strong donor, giving D-π and D-π-D systems and, with Bmes2 as a very strong acceptor, D-π-A system. These compounds exhibit unusual photophysical properties such as emission in the green region of the electromagnetic spectrum in hexane, whereas all other previously reported pyrene derivatives substituted at the 2,7-positions show blue luminescence. Furthermore, spectroelectrochemical measurements suggest very strong coupling between the substituents at the 2,7-positions of pyrene in the D-π-D system. Theoretical studies show that these properties result from the very strong julolidine-type donor and Bmes2 acceptor coupling efficiently to the pyrene HOMO-1 and LUMO+1, respectively. Destabilization of the former and stabilization of the latter lead to an orbital shuffle between HOMO and HOMO 1, and LUMO and LUMO+1 of pyrene. Consequently, the S1 state changes its nature sufficiently enough to gain higher oscillator strength, and the photophysical and electrochemical properties are then greatly influenced by the substituents.
In another project, further derivatives were synthesized with additional acceptor moieties at the K-region of pyrene. These target derivatives exhibit strong bathochromically shifted absorption maxima (519-658 nm), which is a result of the outstanding charge transfer character introduced into the D-π-D pyrene system through the additional acceptor moiety at the K-region. Moreover, emission in the red to NIR region with an emission maximum at 700 nm in CH2Cl2 is detected. The excited state lives unusual long for K-region substituted pyrenes; however, such a lifetime is rather typical for 2,7-substituted pyrene derivatives.
The polycyclic aromatic hydrocarbon perylene, especially perylene diimide, has received considerable attention in recent years and has found use in numerous applications such as dyes, pigments and semiconductors. Nevertheless, it is of fundamental importance to understand how to modulate the electronic and photophysical properties of perylene depending on the specific desired application. Perylenes without carboxyimide groups at the peri positions are much less well studied due to the difficulties in functionalizing the perylene core directly. In particular, only ortho heteroatom substituted perylenes have not been reported thus far (exception: (Bpin)4-Per was already reported by Marder and co-workers). Thus, the effect of substituents on the ortho positions of the perylene core has not been investigated.
Two perylene derivatives were synthesized that bear four strong diphenylamine donor or strong Bmes2 acceptor moieties at the ortho positions. These compounds represent the first examples of perylenes substituted only at the ortho positions with donors or acceptors.
The investigations show that the photophysical and electronic properties of these derivatives are unique and different compared to the well-studied perylene diimides. Thus, up to four reversible reductions or oxidations are possible, which is unprecedented for monomeric perylenes. Furthermore, the photophysical properties of these two ortho-substituted derivatives are unusual compared to reported perylenes on many regards. Thus, large Stokes shifts are obtained, and the singlet excited state of these derivatives lives remarkably long with intrinsic lifetimes of up to 94 ns.
In a cooperation with Dr. Gerard P. McGlacken at University College Cork in Ireland, different quinolones were borylated using an iridium catalyst system to study the electronic and steric effect of the substrates. It was possible to demonstrate that the Ir-catalyzed borylation with the dtbpy ligand allows the direct borylation of various 4-quinolones at the 6- and 7-positions. Thus, later stage functionalization is possible with this method and more highly functionalized quinolones are also compatible with this mild reaction conditions.
Sharpening super-resolution by single molecule localization microscopy in front of a tuned mirror
(2020)
The „Resolution Revolution" in fluorescence microscopy over the last decade has given rise to a variety of techniques that allow imaging beyond the diffraction limit with a resolution power down into the nanometer range. With this, the field of so-called super-resolution microscopy was born. It allows to visualize cellular architecture at a molecular level and thereby achieve a resolution level that had been previously only accessible by electron microscopy approaches.
One of these promising techniques is single molecule localization microscopy (SMLM) in its most varied forms such as direct stochastic optical reconstruction microscopy (dSTORM) which are based on the temporal separation of the emission of individual fluorophores. Localization analysis of the subsequently taken images of single emitters eventually allows to reconstruct an image containing super-resolution information down to typically 20 nm in a cellular setting. The key point here is the localization precision, which mainly depends on the image contrast generated the by the individual fluorophore’s emission. Thus, measures to enhance the signal intensity or reduce the signal background allow to increase the image resolution achieved by dSTORM. In my thesis, this is achieved by simply adding a reflective metal-dielectric nano-coating to the microscopy coverslip that serves as a tunable nano-mirror.
I have demonstrated that such metal-dielectric coatings provide higher photon yield at lower background and thus substantially improve SMLM performance by a significantly increased localization precision, and thus ultimately higher image resolution. The strength of this approach is that ─ except for the coated cover glass ─ no specialized setup is required. The biocompatible metal-dielectric nano-coatings are fabricated directly on microscopy coverslips and have a simple three-ply design permitting straightforward implementation into a conventional fluorescence microscope. The introduced improved lateral resolution with such mirror-enhanced STORM (meSTORM) not only allows to exceed Widefield and Total Internal Reflection Fluorescence (TIRF) dSTORM performance, but also offers the possibility to measure in a simplified setup as it does not require a special TIRF objective lens.
The resolution improvement achieved with meSTORM is both spectrally and spatially tunable and thus allows for dual-color approaches on the one hand, and selectively highlighting region above the cover glass on the other hand, as demonstrated here.
Beyond lateral resolution enhancement, the clear-cut profile of the highlighted region provides additional access to the axial dimension. As shown in my thesis, this allows for example to assess the three-dimensional architecture of the intracellular microtubule network by translating the local localization uncertainty to a relative axial position. Even beyond meSTORM, a wide range of membrane or surface imaging applications may benefit from the selective highlighting and fluorescence enhancing provided by the metal-dielectric nano-coatings. This includes for example, among others, live-cell Fluorescence Correlation Spectroscopy and Fluorescence Resonance Energy Transfer studies as recently demonstrated.
Fluorogenic Aptamers and Fluorescent Nucleoside Analogs as Probes for RNA Structure and Function
(2020)
RNA plays a key role in numerous cellular processes beyond the central dogma of molecular biology. Observing and understanding this wealth of functions, discovering new ones and engineering them into purpose-built tools requires a sensitive means of observation. Over the past decade, fluorogenic aptamers have emerged to fill this niche. These short oligonucleotides are generated by in vitro selection to specifically interact with small organic fluorophores and can be utilized as genetically encoded tags for RNAs of interest.
The most versatile class of fluorogenic aptamers is based on derivatives of hydroxybenzylidene imidazolone (HBI), a conditional fluorophore mimicking the chromophore structure found in green and red fluorescent proteins. The respective aptamers are well-known by the “vegetable” nomenclature, including Spinach, Broccoli and Corn, and have found numerous applications for studying RNA function in vitro and in cells.
Their success, however, is somewhat overshadowed by individual shortcomings such as a propensity for misfolding, dependence on unphysiologically high concentrations of magnesium ions or, in the case of Corn, dimerization that might affect the function of the tagged RNA. Moreover, most fluorogenic aptamers exhibit limited ligand promiscuity by design, thereby restricting their potential for spectral tuning to a narrow window of wavelengths.
This thesis details the characterization of a new fluorogenic aptamer system nicknamed Chili. Chili is derived from an aptamer that was originally selected to bind 4-hydroxy-3,5-dimethoxy¬hydroxy-benzylidene imidazolone (DMHBI), resulting in a green fluorescent complex. Unlike other aptamers of its kind, Chili engages in a proton transfer cycle with the bound ligand, resulting in a remarkably large Stokes shift of more than 130 nm.
By means of an empirical ligand optimization approach, several new DMHBI derivatives were found that bind to Chili with high affinity, furnishing complexes up to 7.5 times brighter compared to the parent ligand. In addition, Chili binds to π-extended DMHBI derivatives that confer fluorescence in the yellow–red region of the visible spectrum. The highest affinity and degree of fluorescence turn-on for both green and red fluorogenic ligands were achieved by the incorporation of a unique, positively charged substituent into the HBI scaffold.
Supplemented by NMR spectroscopy, kinetic and thermodynamic studies showed that the binding site of Chili is loosely preorganized in the absence of ligand and likely forms a G-quadruplex upon ligand binding.
To showcase future applications, Chili was incorporated into a FRET sensor for monitoring the cleavage of an RNA substrate by a 10-23 DNAzyme.
Besides aptamers as macromolecular fluorescent complexes, fluorescent nucleobase analogs are powerful small isomorphic components of RNA suitable for studying structure and folding. Here, the highly emissive nucleobase analog 4-cyanoindole (4CI) was developed into a ribonucleoside (r4CI) for this purpose. A new phosphoramidite building block was synthesized to enable site-specific incorporation of 4CI into RNA.
Thermal denaturation experiments confirmed that 4CI behaves as a universal nucleobase, i.e. without bias towards any particular hybridization partner. Photophysical characterization established r4CI as a generally useful fluorescent ribonucleoside analog. In this work, it was employed to gain further insight into the structure of the Chili aptamer. Using several 4CI-modified Chili–HBI complexes, a novel base–ligand FRET assay was established to obtain a set of combined distance and orientation restraints for the tertiary structure of the aptamer.
In addition to their utility for interrogating structure and binding, supramolecular FRET pairs comprising a fluorescent nucleobase analog donor and an innately fluorogenic acceptor hold great promise for the construction of color-switchable RNA aptamer sensor devices.