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G-quadruplexes (G4s) have been in the focus of research in the last decades for their regulatory roles in vivo and for their use in nano- and biotechnology. However, an understanding of the various factors that drive a particular quadruplex fold remains limited, challenging rational therapeutic targeting and design of these tetrahelical structures. In this regard, insights from modified G-quadruplexes may help to deepen our knowledge of G-quadruplex structure. In this dissertation, sugar-modified guanosine analogs are exploited for their altered conformational preferences regarding both glycosidic bond angle and sugar pucker by their incorporation into different syn positions of the G-core of a model G-quadruplex. Induced structural perturbations as characterized by NMR spectroscopy range from a local change in tetrad polarity to a complete refolding into an unusual structure with a V-shaped loop, a unique G4 structural element in the focus of this work. Detailed conformational analysis of the introduced G analogs and high-resolution structures of the modified quadruplexes reveal a complex interplay of glycosidic torsion angle, sugar pucker preferences and local interactions, which may all play a leading role in driving G4 folding.
Central to this thesis are so-called G-quadruplex (G4) nucleic acids. These unusual structures have recently moved into the scientific limelight - mostly due to their prevalence in the human genome. Incidentally, the vast majority of G4-prone sequences is found in telomeric regions and in the promoter sequences of a large number of cancer-related genes.
Furthermore, recent studies suggest a wide applicability of these structures as therapeutic and functional agents, though the technology is still in its infancy with only a few oligonucleotides in clinical trials. Notably, G-quadruplexes are highly polymorphous, exhibiting different topologies and conformations based on sequence, solution condition and molecularity. Therefore, rational design of such structures with specific, topology-encoded functions demands a comprehensive understanding of the underlying folding parameters.
As the folding process is the result of a whole orchestra of parameters with synergistic effects, the herein proposed approach to understand the G4 structural arrangement concentrates on native G4-forming sequences with well-defined topologies. Perturbations of these structures by rational nucleotide substitutions allow for the observation of discrete effects on the folding pathway and on the resulting overall topology.
The method chosen for primary investigation in the following studies on G4 architectures was Nuclear Magnetic Resonance (NMR) as it is the most powerful tool for structure elucidation in liquids. Unique to this technique, it permits the observation of discrete species in mixtures by distinct perturbations at the atomic level as well as valuable insights into the molecular dynamics.
The included publications study the effects of site-specific bromine substitutions on native quadruplex scaffolds, thereby successfully inducing new structures. These expand the G4 structural landscape but also enhance our understanding of the driving forces in G4 folding.
The four stranded G-quadruplexes are important secondary structures of nucleic acids formed by guanosine-rich sequences. Besides the application as scaffold for technological applications, they are involved in many cellular processes such as gene regulation, replication, or maintenance of chromosomal ends. Characteristically, a large diversity of quadruplex structures is observed, whereas the correlation between sequence and structure is still not fully understood. In this thesis, the effects of modified nucleotides on G-quadruplexes were analyzed using NMR-spectroscopy to gain insight into driving forces determining the folding process. Contrary to DNA quadruplexes, the folding landscape of RNA structures is mostly restricted to parallel topologies. Therefore, ribose moieties were introduced into DNA sequences to isolate the effect of the additional hydroxy group. In this way, sequential CHO hydrogen bonds between the 2′-OH and the H8 of the 3′-neighbored anti conformer were identified and subsequently detected within RNA structures. In a second part, 2′-fluoro-2′-deoxyribose was incorporated at positions with guanosine in unfavored syn orientation. Instead of a changed global fold, the direction of the hydrogen bond network in the modified tetrad was reversed. This first example of tetrad inversion within a unimolecular quadruplex yielded a unique (3+1)-hybrid topology with only homopolar stacking interactions. Additionally, the effect was reproduced for another sequence and high-resolution structures were determined. Unfavored interactions between the 2′-fluorine and the narrow groove of the quadruplex were identified as a reason for different sugar conformations and consequent structural rearrangements.
Adipositas ist medizinisch und sozioökonomisch ein weltweit an Bedeutung gewinnendes Problem. Bariatrische Chirurgie hat sich als effektivste Möglichkeit zur Behandlung morbider Adipositas erwiesen. Dabei ergeben sich deutliche Verbesserungen des diabetischen Stoffwechsels bereits kurz nach dem Eingriff, bevor ein signifikanter Gewichtsverlust eingetreten ist. Die Mechanismen, die dazu führen, sind dabei noch nicht vollständig aufgeklärt. Ziel der Arbeit war es, mit Hilfe des Metabolomikansatzes herauszufinden, ob bariatrische Chirurgie einen Einfluss auf das Metabolom des Urins hat. Dazu wurden Urinproben von 50 Patienten jeweils prä-operativ und bis zu 13 Tage post-operativ mittels 1H-NMR untersucht und mit Hilfe von multivariaten statistischen Methoden analysiert. Dabei konnte deutlich zwischen prä- und post-operativen Proben unterschieden werden. PLS-DA und OPLS-DA Modelle waren in der Lage, 95 % der Spektren richtig in prä- und post-operativ zu klassifizieren. Zur Unterscheidung trugen in erster Linie die Buckets b20, b49 und b50 bei. Bei Betrachtung der gemittelten Spektren fielen eine Heraufregulation in den ppm-Bereichen 1,20-1,24, 2,1-2,5, 3,2-3,6, 4,1-4,2, 7,40-7,45 und 7,6-7,7 sowie eine Herabregulation in den ppm-Bereichen 7,5-7,6 und 7,8-7,9 jeweils post-operativ auf. Bariatrische Chirurgie verändert somit das Metabolom des Urins. Den Variationen im Spektrum liegen Metabolite zu Grunde, deren Identifikation Rückschlüsse auf Stoffwechselprozesse erlauben. Diese können wiederum Erklärungsansätze für den Gewichtsverlust und die Stoffwechselbeeinflussung in Folge einer bariatrischen Chirurgie liefern. Dieses bessere Verständnis der pathophysiologischen Vorgänge könnte weiterhin zur Entwicklung weniger invasiver chirurgischer Eingriffe oder spezieller, individueller pharmakologischer Therapien führen, zielgerichtet auf Gewichtsverlust und Remission des Diabetes mellitus. Weiterhin könnte Metabolomik bei der Entscheidung über die OP-Methode helfen. Dazu müsste es gelingen, aus einem großen Patientenkollektiv mit mehreren OP-Methoden im Urin z.B. einen Prädiktor zu finden, welcher Gewichtsverlust und Resolution von Komorbidität für einen individuellen Patienten vorhersagt. Insgesamt befindet sich die Metabolomikforschung noch in den Anfängen. Im Besonderen gilt dies für die Dokumentation des Einflusses chirurgischer Eingriffe auf das Metabolom des Urins. Weitere Studien mit einem größeren Patientenkollektiv und alternativen Fragestellungen könnten hier zu einem Erkenntnisgewinn führen.