title: A Stably Protonated Adenine Nucleotide with a Highly Shifted pKaValue Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer.
abstract: RNA tertiary structure motifs are stabilized by a wide variety of hydrogen-bonding interactions. Protonated A and C nucleotides are normally not considered to be suitable building blocks for such motifs since their pKavalues are far from physiological pH. Here, we report the NMR solution structure of an in vitro selected GTP-binding RNA aptamer bound to GTP with an intricate tertiary structure. It contains a novel kind of base quartet stabilized by a protonated A residue. Owing to its unique structural environment in the base quartet, the pKavalue for the protonation of this A residue in the complex is shifted by more than 5 pH units compared to the pKafor A nucleotides in single-stranded RNA. This is the largest pKashift for an A residue in structured nucleic acids reported so far, and similar in size to the largest pKashifts observed for amino acid side chains in proteins. Both RNA pre-folding and ligand binding contribute to the pKashift.
authors.affiliation: Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany.
authors.forename: Antje C
authors.initials: AC
authors.lastname: Wolter
authors.affiliation: Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany.
authors.forename: A Katharina
authors.initials: AK
authors.lastname: Weickhmann
authors.affiliation: Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany.
authors.forename: Amir H
authors.initials: AH
authors.lastname: Nasiri
authors.affiliation: Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Hantke
authors.affiliation: Leibniz Institut für Alternsforschung (Fritz-Lipmann-Institut), Beutenbergstrasse 11, 07745, Jena, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Ohlenschläger
authors.affiliation: Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
authors.forename: Christoph H
authors.initials: CH
authors.lastname: Wunderlich
authors.affiliation: Institute of Organic Chemistry, Centre for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
authors.forename: Christoph
authors.initials: C
authors.lastname: Kreutz
authors.affiliation: Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany.
authors.forename: Elke
authors.initials: E
authors.lastname: Duchardt-Ferner
authors.affiliation: Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany.
authors.forename: Jens
authors.identifier: 0000-0001-7193-401X
authors.initials: J
authors.lastname: Wöhnert
mesh_terms: D000227:Adenine Nucleotides / Q000737:chemistry*; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001665:Binding Sites; D006160:Guanosine Triphosphate / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011522:Protons
chemical_list: D000227:Adenine Nucleotides; D052157:Aptamers, Nucleotide; D011522:Protons; D006160:Guanosine Triphosphate
keywords: GTP; NMR spectroscopy; RNA structures; aptamers; protonated adenine