TY  - JOUR
A1  - Ronald, Micura
A1  - Höbartner, Claudia
T1  - Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes
JF  - Chemical Society Reviews
N2  - This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression–regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule – glucosamine-6-phosphate – to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
KW  - Functional nucleic acids
KW  - RNA Enzymes
KW  - RNA labeling
KW  - nucleoside modification recognition
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-212133
ET  - Advance Article
ER  - 
TY  - THES
A1  - Scheitl, Carolin P. M.
T1  - In vitro selected ribozymes for RNA methylation and labeling
T1  - In vitro selektierte Ribozyme für Methylierung und Markierung von RNA
N2  - The focus of this work was the development and application of highly efficient RNA catalysts for the site-specific modification of RNA with special focus on methylation. In the course of this thesis, the first methyltransferase ribozyme (MTR1), which uses m6G as the methyl group donor was developed and further characterized. The RNA product was identified as the natural modification m1A. X-Ray crystallography was used to solve the 3D structure of the ribozyme, which directly suggested a plausible reaction meachnism. The MTR1 ribozyme was also successfully repurposed for a nucleobase transformation reaction of a purine nucleoside. This resulted in a formyl-imidazole moiety directly on the intact RNA, which was directly used for further bioconjugation reactions. Finally, additional selections and reselections led to the identification of highly active alkyltransferase ribozymes that can be used for the labeling of various RNA targets
N2  - Der Schwerpunkt dieser Arbeit lag auf der Entwicklung sowie Anwendung hocheffizienter RNA-Katalysatoren für die positionsspezifische Modifikation von RNA mit besonderem Fokus auf Methylierungen. Im Rahmen dieser Arbeit wurde das erste Methyltransferase-Ribozym (MTR1), das m6G als Methylgruppendonor verwendet, entwickelt und näher charakterisiert. Das RNA-Produkt wurde als die natürliche Modifikation m1A identifiziert. Mit Hilfe der Röntgenkristallographie wurde des Weiteren die 3D-Struktur des Ribozyms aufgeklärt, was direkt auf ein plausibles Reaktionsmuster schließen ließ. Das MTR1-Ribozym wurde zudem erfolgreich für eine Nukleobasen-Transformationsreaktion eines Purins verwendet, bei der eine Formyl-Imidazol-Einheit direkt an der intakten RNA gebildet wird. Dieses Reaktionsprodukt wurde für positionsgenaue Biokonjugationsreaktionen verwendet. Schließlich führten zusätzliche Selektionen und weitere Reselektionen zur Identifizierung hochaktiver Alkyltransferase-Ribozyme, die für die Markierung verschiedener Ziel-RNAs verwendet werden können.
KW  - RNA labeling
KW  - Methyltransferase
KW  - Methylierung
KW  - Ribozym
KW  - SELEX
Y1  - 2023
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-330049
ER  -