title: Post-synthetic Spin-Labeling of RNA through Click Chemistry for PELDOR Measurements.
abstract: Site-directed spin labeling of RNA based on click chemistry is used in combination with pulsed electron-electron double resonance (PELDOR) to benchmark a nitroxide spin label, called here dŲ. We compare this approach with another established method that employs the rigid spin label Çm for RNA labeling. By using CD spectroscopy, thermal denaturation measurements, CW-EPR as well as PELDOR we analyzed and compared the influence of dŲ and Çm on a self-complementary RNA duplex. Our results demonstrate that the conformational diversity of dŲ is significantly reduced near the freezing temperature of a phosphate buffer, resulting in strongly orientation-selective PELDOR time traces of the dŲ-labeled RNA duplex.
authors.affiliation: Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Kerzhner
authors.affiliation: Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.
authors.forename: Dinar
authors.initials: D
authors.lastname: Abdullin
authors.affiliation: Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Więcek
authors.affiliation: Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.
authors.forename: Hideto
authors.initials: H
authors.lastname: Matsuoka
authors.affiliation: Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany.
authors.forename: Gregor
authors.initials: G
authors.lastname: Hagelueken
authors.affiliation: Institute for Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115, Bonn, Germany. schiemann@pc.uni-bonn.de.
authors.forename: Olav
authors.initials: O
authors.lastname: Schiemann
authors.affiliation: Life & Medical Sciences Institute, Chemical Biology & Medicinal Chemistry Unit c/o Kekulé-Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany. m.famulok@uni-bonn.de.|Max-Planck Fellow Group Chemical Biology, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany. m.famulok@uni-bonn.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Famulok
mesh_terms: D057930:Click Chemistry / Q000379:methods*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods; D004583:Electrons; D012313:RNA; D013113:Spin Labels / Q000138:chemical synthesis*
chemical_list: D013113:Spin Labels; D012313:RNA
keywords: EPR spectroscopy; RNA structures; conformation analysis; oligonucleotides; spin label