title: Fluorogenic Labeling of 5-Formylpyrimidine Nucleotides in DNA and RNA.
abstract: 5-Formylcytosine (5fC) and 5-formyluracil (5fU) are natural nucleobase modifications that are generated by oxidative modification of 5-methylcytosine and thymine (or 5-methyluracil). Herein, we describe chemoselective labeling of 5-formylpyrimidine nucleotides in DNA and RNA by fluorogenic aldol-type condensation reactions with 2,3,3-trimethylindole derivatives. Mild and specific reaction conditions were developed for 5fU and 5fC to produce hemicyanine-like chromophores with distinct photophysical properties. Residue-specific detection was established by fluorescence readout as well as primer-extension assays. The reactions were optimized on DNA oligonucleotides and were equally suitable for the modification of 5fU- and 5fC-modified RNA. This direct labeling approach of 5-formylpyrimidines is expected to help in elucidating the occurrence, enzymatic transformations, and functional roles of these epigenetic/epitranscriptomic nucleobase modifications in DNA and RNA.
authors.affiliation: Institute for Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany.|Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.|Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
authors.forename: Biswajit
authors.initials: B
authors.lastname: Samanta
authors.affiliation: Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Seikowski
authors.affiliation: Institute for Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany. claudia.hoebartner@chemie.uni-goettingen.de.|Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany. claudia.hoebartner@chemie.uni-goettingen.de.|Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany. claudia.hoebartner@chemie.uni-goettingen.de.
authors.forename: Claudia
authors.initials: C
authors.lastname: Höbartner
mesh_terms: D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*
chemical_list: D005456:Fluorescent Dyes; D011742:Pyrimidine Nucleotides; D012313:RNA; D004247:DNA
keywords: DNA; RNA; epigenetics; fluorogenic probes; modified nucleobases