@phdthesis{Steinmetzger2020,
  author    = {Steinmetzger, Christian},
  title     = {Fluorogenic Aptamers and Fluorescent Nucleoside Analogs as Probes for RNA Structure and Function},
  doi       = {10.25972/OPUS-20760},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-207604},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {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.},
  subject      = {Aptamer},
  language  = {en}
}
@phdthesis{Juling2010,
  author    = {Juling, Martin Johannes},
  title     = {Untersuchung der HBV-Genotypen bei antiviral behandelten Hepatitis B-Patienten im Zeitraum von 1997 bis 2004 an der Universit{\"a}tsklinik W{\"u}rzburg},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48789},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Von den acht bekannten HBV-Genotypen sind die Genotypen A und D in Europa vorherrschend, Genotyp A in Nordwesteuropa, Genotyp D im Mittelmeerraum und in S{\"u}dosteuropa. Dies best{\"a}tigte sich auch in der vorliegenden Studie, bei der von 62 genotypisierten Proben 91,9 \% diesen beiden Genotypen zugeordnet werden konnten. Genotyp D war mit 64,5 \% (40 Patienten) vorherrschend. Es folgten der Genotyp A (17 Patienten) und der Genotyp C (4 Patienten). In einem Fall wurde Genotyp B nachgewiesen. Deutschland als Herkunftsland war bei Patienten mit Genotyp A signifikant h{\"a}ufiger vertreten als bei Patienten mit Genotyp D. Der relativ hohe Genotyp D-Anteil ist m{\"o}glicherweise darauf zur{\"u}ckzuf{\"u}hren, dass durch zunehmende Immigration das Auftreten verschiedener Genotypen beispielsweise aus dem s{\"u}dosteurop{\"a}ischen Raum beg{\"u}nstigt wird. Patienten mit Genotyp A sprechen h{\"a}ufig besser auf IFN-alpha an, so dass eine Therapie mit Nukleosid- bzw. Nukleotidanaloga nicht erforderlich ist. Diese Patienten wurden somit {\`a} priori nicht in dieser Studie erfasst, was eine m{\"o}gliche Erkl{\"a}rung daf{\"u}r ist, dass der Genotyp A-Anteil mit 27,4 \% relativ gering ausfiel. Bei der Untersuchung von statistischen Zusammenh{\"a}ngen zwischen HBV-Genotyp und Patientenalter, Geschlecht, Viruslast und Therapiedauer ergaben sich keine signifikanten Ergebnisse. Diese Studie bietet Basisinformationen zur Genotypverteilung in Deutschland. Bez{\"u}glich einer Korrelation zwischen den verschiedenen HBV-Genotypen und demographischen, virologischen sowie klinischen Charakteristika wird es k{\"u}nftig weiterer Studien bed{\"u}rfen.},
  subject      = {Hepatitis B},
  language  = {de}
}