@article{HoernesFaserlJuenetal.2018,
  author    = {Hoernes, Thomas Philipp and Faserl, Klaus and Juen, Michael Andreas and Kremser, Johannes and Gasser, Catherina and Fuchs, Elisabeth and Shi, Xinying and Siewert, Aaron and Lindner, Herbert and Kreutz, Christoph and Micura, Ronald and Joseph, Simpson and H{\"o}bartner, Claudia and Westhof, Eric and H{\"u}ttenhofer, Alexander and Erlacher, Matthias David},
  title     = {Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions},
  series = {Nature Communications},
  volume    = {9},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-018-07321-8},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-321067},
  year      = {2018},
  abstract  = {The precise interplay between the mRNA codon and the tRNA anticodon is crucial for ensuring efficient and accurate translation by the ribosome. The insertion of RNA nucleobase derivatives in the mRNA allowed us to modulate the stability of the codon-anticodon interaction in the decoding site of bacterial and eukaryotic ribosomes, allowing an in-depth analysis of codon recognition. We found the hydrogen bond between the N1 of purines and the N3 of pyrimidines to be sufficient for decoding of the first two codon nucleotides, whereas adequate stacking between the RNA bases is critical at the wobble position. Inosine, found in eukaryotic mRNAs, is an important example of destabilization of the codon-anticodon interaction. Whereas single inosines are efficiently translated, multiple inosines, e.g., in the serotonin receptor 5-HT2C mRNA, inhibit translation. Thus, our results indicate that despite the robustness of the decoding process, its tolerance toward the weakening of codon-anticodon interactions is limited.},
  language  = {en}
}
@unpublished{SeitzJungnickelKleiberetal.2024,
  author    = {Seitz, Florian and Jungnickel, Tina and Kleiber, Nicole and Kretschmer, Jens and Dietzsch, Julia and Adelmann, Juliane and Bohnsack, Katherine E. and Bohnsack, Markus T. and H{\"o}bartner, Claudia},
  title     = {Atomic mutagenesis of N\(^6\)-methyladenosine reveals distinct recognition modes by human m\(^6\)A reader and eraser proteins},
  series = {Journal of the American Chemical Society},
  journal   = {Journal of the American Chemical Society},
  doi       = {10.1021/jacs.4c00626},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-352376},
  year      = {2024},
  abstract  = {N\(^6\)-methyladenosine (m\(^6\)A) is an important modified nucleoside in cellular RNA associated with multiple cellular processes and is implicated in diseases. The enzymes associated with the dynamic installation and removal of m\(^6\)A are heavily investigated targets for drug research, which requires detailed knowledge of the recognition modes of m\(^6\)A by proteins. Here, we use atomic mutagenesis of m\(^6\)A to systematically investigate the mechanisms of the two human m\(^6\)A demethylase enzymes FTO and ALKBH5 and the binding modes of YTH reader proteins YTHDF2/DC1/DC2. Atomic mutagenesis refers to atom-specific changes that are introduced by chemical synthesis, such as the replacement of nitrogen by carbon atoms. Synthetic RNA oligonucleotides containing site-specifically incorporated 1-deaza-, 3-deaza-, and 7-deaza-m\(^6\)A nucleosides were prepared by solid-phase synthesis and their RNA binding and demethylation by recombinant proteins were evaluated. We found distinct differences in substrate recognition and transformation and revealed structural preferences for the enzymatic activity. The deaza m\(^6\)A analogues introduced in this work will be useful probes for other proteins in m\(^6\)A research.},
  language  = {en}
}
@article{OkudaLenzSeitzetal.2023,
  author    = {Okuda, Takumi and Lenz, Ann-Kathrin and Seitz, Florian and Vogel, J{\"o}rg and H{\"o}bartner, Claudia},
  title     = {A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells},
  series = {Nature Chemistry},
  journal   = {Nature Chemistry},
  doi       = {10.1038/s41557-023-01320-z},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328762},
  year      = {2023},
  abstract  = {Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.},
  language  = {en}
}
@unpublished{NeitzHoebartner2023,
  author    = {Neitz, Hermann and H{\"o}bartner, Claudia},
  title     = {A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker},
  series = {Chemical Communications},
  journal   = {Chemical Communications},
  edition   = {submitted version},
  doi       = {10.1039/D3CC03796G},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328255},
  year      = {2023},
  abstract  = {We report the fluorescent nucleoside ToldU and its application as a photoresponsive crosslinker in three different DNA architectures with enhanced fluorescence emission of the crosslinked products. The fluorogenic ToldU crosslinking reaction enables the assembly of DNA polymers in a hybridization chain reaction for the concentration-dependent detectio of a specific DNA sequence.},
  language  = {en}
}
@unpublished{DietzschJayachandranMuelleretal.2023,
  author    = {Dietzsch, Julia and Jayachandran, Ajay and Mueller, Stefan and H{\"o}bartner, Claudia and Brixner, Tobias},
  title     = {Excitonic coupling of RNA-templated merocyanine dimer studied by higher-order transient absorption spectroscopy},
  series = {Chemical Communications},
  journal   = {Chemical Communications},
  edition   = {submitted version},
  doi       = {10.1039/D3CC02024J},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-327772},
  year      = {2023},
  abstract  = {We report the synthesis and spectroscopic analysis of RNA containing the barbituric acid merocyanine rBAM2 as a nucleobase surrogate. Incorporation into RNA strands by solid-phase synthesis leads to fluorescence enhancement compared to the free chromophore. In addition, linear absorption studies show the formation of an excitonically coupled H-type dimer in the hybridized duplex. Ultrafast third- and fifth-order transient absorption spectroscopy of this non-fluorescent dimer suggests immediate (sub-200 fs) exciton transfer and annihilation due to the proximity of the rBAM2 units.},
  language  = {en}
}
@article{ScheitlOkudaAdelmannetal.2023,
  author    = {Scheitl, Carolin P. M. and Okuda, Takumi and Adelmann, Juliane and H{\"o}bartner, Claudia},
  title     = {Ribozyme-catalyzed late-stage functionalization and fluorogenic labeling of RNA},
  series = {Angewandte Chemie International Edition},
  volume    = {62},
  journal   = {Angewandte Chemie International Edition},
  doi       = {10.1002/anie.202305463},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-327543},
  year      = {2023},
  abstract  = {Site-specific introduction of biorthogonal handles into RNAs is in high demand for decorating RNAs with fluorophores, affinity labels or other modifications. Aldehydes represent attractive functional groups for post-synthetic bioconjugation reactions. Here, we report a ribozyme-based method for the synthesis of aldehyde-functionalized RNA by directly converting a purine nucleobase. Using the methyltransferase ribozyme MTR1 as an alkyltransferase, the reaction is initiated by site-specific N1 benzylation of purine, followed by nucleophilic ring opening and spontaneous hydrolysis under mild conditions to yield a 5-amino-4-formylimidazole residue in good yields. The modified nucleotide is accessible to aldehyde-reactive probes, as demonstrated by the conjugation of biotin or fluorescent dyes to short synthetic RNAs and tRNA transcripts. Upon fluorogenic condensation with a 2,3,3-trimethylindole, a novel hemicyanine chromophore was generated directly on the RNA. This work expands the MTR1 ribozyme's area of application from a methyltransferase to a tool for site-specific late-stage functionalization of RNA.},
  language  = {en}
}
@article{LiuVonhausenSchulzetal.2022,
  author    = {Liu, Bin and Vonhausen, Yvonne and Schulz, Alexander and H{\"o}bartner, Claudia and W{\"u}rthner, Frank},
  title     = {Peptide Backbone Directed Self-Assembly of Merocyanine Oligomers into Duplex Structures},
  series = {Angewandte Chemie International Edition},
  volume    = {61},
  journal   = {Angewandte Chemie International Edition},
  number    = {21},
  doi       = {10.1002/anie.202200120},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-318797},
  year      = {2022},
  abstract  = {The pseudopeptide backbone provided by N-(2-aminoethyl)-glycine oligomers with attached nucleobases has been widely utilized in peptide nucleic acids (PNAs) as DNA mimics. Here we demonstrate the suitability of this backbone for the formation of structurally defined dye stacks. Toward this goal a series of peptide merocyanine (PMC) dye oligomers connected to a N-(2-aminoethyl)-glycine backbone were prepared through peptide synthesis. Our concentration-, temperature- and solvent-dependent UV/Vis absorption studies show that under the control of dipole-dipole interactions, smaller-sized oligomers consisting of one, two or three dyes self-assemble into defined duplex structures containing two up to six chromophores. In contrast, upon further extension of the oligomer, the chosen peptide backbone cannot direct the formation of a defined duplex architecture anymore due to intramolecular aggregation between the dyes. For all aggregate species a moderate aggregation-induced emission enhancement is observed.},
  language  = {en}
}
@article{NeitzBessiKachleretal.2022,
  author    = {Neitz, Hermann and Bessi, Irene and Kachler, Valentin and Michel, Manuela and H{\"o}bartner, Claudia},
  title     = {Tailored tolane-perfluorotolane assembly as supramolecular base pair replacement in DNA},
  series = {Angewandte Chemie International Edition},
  volume    = {62},
  journal   = {Angewandte Chemie International Edition},
  number    = {1},
  doi       = {10.1002/anie.202214456},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-312575},
  year      = {2022},
  abstract  = {Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.},
  language  = {en}
}
@unpublished{NeitzBessiKuperetal.2023,
  author    = {Neitz, Hermann and Bessi, Irene and Kuper, Jochen and Kisker, Caroline and H{\"o}bartner, Claudia},
  title     = {Programmable DNA interstrand crosslinking by alkene-alkyne [2+2] photocycloaddition},
  series = {Journal of the American Chemical Society},
  journal   = {Journal of the American Chemical Society},
  edition   = {submitted version},
  doi       = {10.1021/jacs.3c01611},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-311822},
  year      = {2023},
  abstract  = {Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (\(^{Phe}\)dU). The crosslinking ability of \(^{Phe}\)dU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2+2] cycloaddition within the DNA duplex, resulting in efficient formation of a \(^{Phe}\)dU-dimer after short irradiation times of a few seconds. A \(^{Phe}\)dU dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.},
  language  = {en}
}
@incollection{LiaqatSednevHoebartner2022,
  author    = {Liaqat, Anam and Sednev, Maksim V. and H{\"o}bartner, Claudia},
  title     = {In Vitro Selection of Deoxyribozymes for the Detection of RNA Modifications},
  series = {Ribosome Biogenesis: Methods and Protocols},
  booktitle = {Ribosome Biogenesis: Methods and Protocols},
  publisher = {Humana Press},
  isbn      = {978-1-0716-2501-9},
  doi       = {10.1007/978-1-0716-2501-9_10},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-279208},
  publisher      = {Universit{\"a}t W{\"u}rzburg},
  pages     = {167-179},
  year      = {2022},
  abstract  = {Deoxyribozymes are artificially evolved DNA molecules with catalytic abilities. RNA-cleaving deoxyribozymes have been recognized as an efficient tool for detection of modifications in target RNAs and provide an alternative to traditional and modern methods for detection of ribose or nucleobase methylation. However, there are only few examples of DNA enzymes that specifically reveal the presence of a certain type of modification, including N6-methyladenosine, and the knowledge about how DNA enzymes recognize modified RNAs is still extremely limited. Therefore, DNA enzymes cannot be easily engineered for the analysis of desired RNA modifications, but are instead identified by in vitro selection from random DNA libraries using synthetic modified RNA substrates. This protocol describes a general in vitro selection stagtegy to evolve new RNA-cleaving DNA enzymes that can efficiently differentiate modified RNA substrates from their unmodified counterpart.},
  language  = {en}
}