title: Direct ¹³C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA.
abstract: In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond (1)H detection. Here, we develop (13)C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for (13)C direct detection allows correlations of donor-acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed (13)C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics.
authors: Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max von Laue-Str. 7, 60438, Frankfurt, Germany. fuertig@nmr.uni-frankfurt.de.
authors: Boris
authors: http://orcid.org/0000-0001-6443-7656
authors: B
authors: Fürtig
authors: Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max von Laue-Str. 7, 60438, Frankfurt, Germany.
authors: Robbin
authors: R
authors: Schnieders
authors: Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max von Laue-Str. 7, 60438, Frankfurt, Germany.
authors: Christian
authors: C
authors: Richter
authors: Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max von Laue-Str. 7, 60438, Frankfurt, Germany.
authors: Heidi
authors: H
authors: Zetzsche
authors: Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max von Laue-Str. 7, 60438, Frankfurt, Germany.
authors: Sara
authors: S
authors: Keyhani
authors: Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max von Laue-Str. 7, 60438, Frankfurt, Germany.
authors: Christina
authors: C
authors: Helmling
authors: Bruker BioSpin, Industriestrasse 26, 8117, Fällanden, Switzerland.
authors: Helena
authors: H
authors: Kovacs
authors: Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universität Frankfurt, Max von Laue-Str. 7, 60438, Frankfurt, Germany. schwalbe@nmr.uni-frankfurt.de.
authors: Harald
authors: H
authors: Schwalbe
mesh_terms: D020029:Base Pairing; D066241:Carbon-13 Magnetic Resonance Spectroscopy; D006859:Hydrogen / Q000737:chemistry; D006860:Hydrogen Bonding; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA; D006859:Hydrogen
keywords: 13C direct detection; Base pairs; Exchange; Hydrogen bonds; RNA