@unpublished{SeitzJungnickelKleiberetal.2024,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}
}
@unpublished{DietzschJayachandranMuelleretal.2023,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}
}
@phdthesis{Dietzsch2022,
  author    = {Dietzsch, Julia},
  title     = {Nucleic acid-mediated fluorescence activation and chromophore assembly},
  doi       = {10.25972/OPUS-25976},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259761},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {Nucleic acids are not only one of the most important classes of macromolecules in biochemistry but also a promising platform for the defined arrangement of chromophores. Thanks to their precise organization by directional polar and hydrophobic interactions, oligonucleotides can be exploited as suitable templates for multichromophore assemblies with predictable properties. To expand the toolbox of emissive, base pairing nucleobase analogs several barbituric acid merocyanine (BAM) chromophores with tunable spectroscopic properties were synthesized and incorporated into RNA, DNA and glycol nucleic acid (GNA) oligonucleotides. A multitude of duplexes containing up to ten BAM chromophores was obtained and analysis by spectroscopic methods revealed the presence of dipolarly coupled merocyanine aggregates with properties strongly dependent on the chromophore orientation toward each other and the backbone conformation. These characteristics were exploited for various applications such as FRET pair formation and polymerase chain reaction (PCR) experiments. The observed formation of higher-order aggregates implies future applications of these new oligonucleotide-chromophore systems as light-harvesting DNA nanomaterials. Besides oligonucleotide templated covalent assembly of chromophores also non-covalent nucleic acid-chromophore complexes are a broad field of research. Among these, fluorogenic RNA aptamers are of special interest with the most versatile ones based on derivatives of the GFP chromophore hydroxybenzylidene imidazolone (HBI). Therefore, new HBI-derived chromophores with an expanded conjugated system and an additional exocyclic amino group for an enhanced binding affinity were synthesized and analyzed in complex with the Chili aptamer. Among these, structurally new fluorogenes with strong fluorescence activation upon binding to Chili were identified which are promising for further derivatization and application as color-switching sensor devices for example.},
  subject      = {Nucleins{\"a}uren},
  language  = {en}
}
@article{DietzschBialasBandorfetal.2022,
  author    = {Dietzsch, Julia and Bialas, David and Bandorf, Johannes and W{\"u}rthner, Frank and H{\"o}bartner, Claudia},
  title     = {Tuning Exciton Coupling of Merocyanine Nucleoside Dimers by RNA, DNA and GNA Double Helix Conformations},
  series = {Angewandte Chemie International Edition},
  journal   = {Angewandte Chemie International Edition},
  doi       = {10.1002/anie.202116783},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-254565},
  pages     = {e202116783},
  year      = {2022},
  abstract  = {Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, - stacking and hydrogen-bonding interactions. The realized supramolecular motifs include hydrogenbonded BAM-adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.},
  language  = {en}
}