title: Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy.
abstract: In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids.
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
authors.forename: Michael Andreas
authors.initials: MA
authors.lastname: Juen
authors.affiliation: Bachem Americas, Inc., 3132 Kashiwa Street, Torrance, CA 90505, USA.
authors.forename: Christoph Hermann
authors.initials: CH
authors.lastname: Wunderlich
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
authors.forename: Felix
authors.initials: F
authors.lastname: Nußbaumer
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
authors.forename: Martin
authors.initials: M
authors.lastname: Tollinger
authors.affiliation: Computational Biology and Biomolecular NMR, Max F. Perutz Laboratories (MFPL), University of Vienna, Dr. Bohr Gasse 9 (VBC 5), 1030, Vienna, Austria.
authors.forename: Georg
authors.initials: G
authors.lastname: Kontaxis
authors.affiliation: Computational Biology and Biomolecular NMR, Max F. Perutz Laboratories (MFPL), University of Vienna, Dr. Bohr Gasse 9 (VBC 5), 1030, Vienna, Austria.
authors.forename: Robert
authors.initials: R
authors.lastname: Konrat
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Room 612, Gower Street, London, WC1E 6BT, UK. d.hansen@ucl.ac.uk.
authors.forename: D Flemming
authors.identifier: 0000-0003-0891-220X
authors.initials: DF
authors.lastname: Hansen
authors.affiliation: Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria. christoph.kreutz@uibk.ac.at.
authors.forename: Christoph
authors.identifier: 0000-0002-7018-9326
authors.initials: C
authors.lastname: Kreutz
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D007553:Isotope Labeling / Q000379:methods*; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009690:Nucleic Acid Conformation; D011522:Protons; D012313:RNA / Q000737:chemistry*
chemical_list: D011522:Protons; D012313:RNA; D004247:DNA
keywords: DNA; NMR spectroscopy; RNA; proton relaxation dispersion; stable isotope labeling