@article{SteinmetzgerBaeuerleinHoebartner2020, author = {Steinmetzger, Christian and B{\"a}uerlein, Carmen and H{\"o}bartner, Claudia}, title = {Supramolecular fluorescence resonance energy transfer in nucleobase-modified fluorogenic RNA aptamers}, series = {Angewandte Chemie, International Edition}, volume = {59}, journal = {Angewandte Chemie, International Edition}, doi = {10.1002/anie.201916707}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-203084}, pages = {6760-6764}, year = {2020}, abstract = {RNA aptamers form compact tertiary structures and bind their ligands in specific binding sites. Fluorescence-based strategies reveal information on structure and dynamics of RNA aptamers. Here we report the incorporation of the universal emissive nucleobase analog 4-cyanoindole into the fluorogenic RNA aptamer Chili, and its application as a donor for supramolecular FRET to bound ligands DMHBI+ or DMHBO+. The photophysical properties of the new nucleobase-ligand-FRET pair revealed structural restraints for the overall RNA aptamer organization and identified nucleotide positions suitable for FRET-based readout of ligand binding. This strategy is generally suitable for binding site mapping and may also be applied for responsive aptamer devices.}, language = {en} } @unpublished{ScheitlGhaemMaghamiLenzetal.2020, author = {Scheitl, Carolin P.M. and Ghaem Maghami, Mohammad and Lenz, Ann-Kathrin and H{\"o}bartner, Claudia}, title = {Site-specific RNA methylation by a methyltransferase ribozyme}, series = {Nature}, journal = {Nature}, doi = {10.1038/s41586-020-2854-z}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-218687}, year = {2020}, abstract = {Nearly all classes of coding and non-coding RNA undergo post-transcriptional modification including RNA methylation. Methylated nucleotides belong to the evolutionarily most conserved features of tRNA and rRNA.1,2 Many contemporary methyltransferases use the universal cofactor S-adenosylmethionine (SAM) as methyl group donor. This and other nucleotide-derived cofactors are considered as evolutionary leftovers from an RNA World, in which ribozymes may have catalysed essential metabolic reactions beyond self-replication.3 Chemically diverse ribozymes seem to have been lost in Nature, but may be reconstructed in the laboratory by in vitro selection. Here, we report a methyltransferase ribozyme that catalyses the site-specific installation of 1-methyladenosine (m1A) in a substrate RNA, utilizing O6-methylguanine (m6G) as a small-molecule cofactor. The ribozyme shows a broad RNA sequence scope, as exemplified by site-specific adenosine methylation in tRNAs. This finding provides fundamental insights into RNA's catalytic abilities, serves a synthetic tool to install m1A in RNA, and may pave the way to in vitro evolution of other methyltransferase and demethylase ribozymes.}, language = {en} } @article{MaghamiDeyLenzetal.2020, author = {Maghami, Mohammad Ghaem and Dey, Surjendu and Lenz, Ann-Kathrin and H{\"o}bartner, Claudia}, title = {Repurpsing Antiviral Drugs for Orthogonal RNA-Catalyzed Labeling}, series = {Angewandte Chemie, International Edition}, volume = {59}, journal = {Angewandte Chemie, International Edition}, doi = {10.1002/anie.202001300}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-205552}, pages = {9335-9339}, year = {2020}, abstract = {In vitro selected ribozymes are promising tools for site-specific labeling of RNA. Previously known nucleic acid catalysts attached fluorescently labeled adenosine or guanosine derivatives through 2',5'-branched phosphodiester bonds to the RNA of interest. Herein, we report new ribozymes that use orthogonal substrates, derived from the antiviral drug tenofovir, and attach bioorthogonal functional groups, as well as affinity handles and fluorescent reporter units through a hydrolytically more stable phosphonate ester linkage. The tenofovir transferase ribozymes were identified by in vitro selection and are orthogonal to nucleotide transferase ribozymes. As genetically encodable functional RNAs, these ribozymes may be developed for potential cellular applications. The orthogonal ribozymes addressed desired target sites in large RNAs in vitro, as shown by fluorescent labeling of E. coli 16S and 23S RNAs in total cellular RNA.}, language = {en} } @article{ScheitlLangeHoebartner2020, author = {Scheitl, Carolin P. M. and Lange, Sandra and H{\"o}bartner, Claudia}, title = {New deoxyribozymes for the native ligation of RNA}, series = {Molecules}, volume = {25}, journal = {Molecules}, number = {16}, doi = {https://doi.org/10.3390/molecules25163650}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-210405}, year = {2020}, abstract = {Deoxyribozymes (DNAzymes) are small, synthetic, single-stranded DNAs capable of catalysing chemical reactions, including RNA ligation. Herein, we report a novel class of RNA ligase deoxyribozymes that utilize 5'-adenylated RNA (5'-AppRNA) as the donor substrate, mimicking the activated intermediates of protein-catalyzed RNA ligation. Four new DNAzymes were identified by in vitro selection from an N40 random DNA library and were shown to catalyze the intermolecular linear RNA-RNA ligation via the formation of a native 3'-5'-phosphodiester linkage. The catalytic activity is distinct from previously described RNA-ligating deoxyribozymes. Kinetic analyses revealed the optimal incubation conditions for high ligation yields and demonstrated a broad RNA substrate scope. Together with the smooth synthetic accessibility of 5'-adenylated RNAs, the new DNA enzymes are promising tools for the protein-free synthesis of long RNAs, for example containing precious modified nucleotides or fluorescent labels for biochemical and biophysical investigations.}, language = {en} } @article{LiaqatStillerMicheletal.2020, author = {Liaqat, Anam and Stiller, Carina and Michel, Manuela and Sednev, Maksim V. and H{\"o}bartner, Claudia}, title = {N\(^6\)-Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes}, series = {Angewandte Chemie International Edition}, journal = {Angewandte Chemie International Edition}, edition = {Early View}, doi = {10.1002/ange.202006218}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212121}, year = {2020}, abstract = {RNA-cleaving deoxyribozymes can serve as selective sensors and catalysts to examine the modification state of RNA. However, site-specific endonuclease deoxyribozymes that selectively cleave posttranscriptionally modified RNA are extremely rare and their specificity over unmodified RNA is low. In this study, we report that the native tRNA modification N\(^6\)-isopentenyladenosine (i\(^6\)A) strongly enhances the specificity and has the power to reconfigure the active site of an RNA-cleaving deoxyribozyme. Using in vitro selection, we identified a DNA enzyme that cleaves i\(^6\)A-modified RNA at least 2500-fold faster than unmodified RNA. Another deoxyribozyme shows unique and unprecedented behaviour by shifting its cleavage site in the presence of the i\(^6\)A RNA modification. Together with deoxyribozymes that are strongly inhibited by i\(^6\)A, these results highlight intricate ways of modulating the catalytic activity of DNA by posttranscriptional RNA modifications.}, language = {en} } @article{RonaldHoebartner2020, author = {Ronald, Micura and H{\"o}bartner, Claudia}, title = {Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes}, series = {Chemical Society Reviews}, journal = {Chemical Society Reviews}, edition = {Advance Article}, doi = {10.1039/D0CS00617C}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212133}, year = {2020}, abstract = {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.}, language = {en} }