@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{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{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{LiaqatSednevStilleretal.2021,
  author    = {Liaqat, Anam and Sednev, Maksim V. and Stiller, Carina and H{\"o}bartner, Claudia},
  title     = {RNA-cleaving deoxyribozymes differentiate methylated cytidine isomers in RNA},
  series = {Angewandte Chemie International Edition},
  volume    = {60},
  journal   = {Angewandte Chemie International Edition},
  doi       = {10.1002/anie.202106517},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-256519},
  pages     = {19058-19062},
  year      = {2021},
  abstract  = {Deoxyribozymes are emerging as modification-specific endonucleases for the analysis of epigenetic RNA modifications. Here, we report RNA-cleaving deoxyribozymes that differentially respond to the presence of natural methylated cytidines, 3-methylcytidine (m\(^3\)C), N\(^4\)-methylcytidine (m\(^4\)C), and 5-methylcytidine (m\(^5\)C), respectively. Using in vitro selection, we found several DNA catalysts, which are selectively activated by only one of the three cytidine isomers, and display 10- to 30-fold accelerated cleavage of their target m\(^3\)C-, m\(^4\)C- or m\(^5\)C-modified RNA. An additional deoxyribozyme is strongly inhibited by any of the three methylcytidines, but effectively cleaves unmodified RNA. The mXC-detecting deoxyribozymes are programmable for the interrogation of natural RNAs of interest, as demonstrated for human mitochondrial tRNAs containing known m\(^3\)C and m\(^5\)C sites. The results underline the potential of synthetic functional DNA to shape highly selective active sites.},
  language  = {en}
}