title: RNA SHAPE chemistry with aromatic acylating reagents.
abstract: As chemical methods for RNA secondary structure determination, SHAPE chemistry (selective 2'-hydroxyl acylation analyzed by primer extension) has been developed to specifically target flexible nucleotides (often unpaired nucleotides) independently to their purine or pyrimidine nature. In order to improve the specificity of acylating reagents towards unpaired nucleotides, we have explored the reactivity of symmetric anhydrides, acyl fluorides, active esters like succinimidyl ester and cyanomethyl esters for 2'-O-acylation reaction. Among the tested compounds, only the acyl fluoride 4 showed a low reactivity (compared to NMIA). However, this study is the first to show that nucleophilic catalysts like DMAP greatly improved the selective 2'-hydroxyl acylation by symmetric anhydrides, acyl fluorides and succinimidyl ester, with the 2-fluorobenzoic anhydride 5 being the most reactive.
authors.affiliation: PPSM, CNRS, Institut d'Alembert, ENS de Cachan, 61 Avenue du P(t) Wilson, F-94235 Cachan, France.
authors.forename: Laura
authors.initials: L
authors.lastname: Nodin
authors.affiliation: PPSM, CNRS, Institut d'Alembert, ENS de Cachan, 61 Avenue du P(t) Wilson, F-94235 Cachan, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Noël
authors.affiliation: LBPA, CNRS, Institut d'Alembert, ENS de Cachan, 61 Avenue du P(t) Wilson, F-94235 Cachan, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Chaminade
authors.affiliation: LBPA, CNRS, Institut d'Alembert, ENS de Cachan, 61 Avenue du P(t) Wilson, F-94235 Cachan, France.
authors.forename: Ouerdia
authors.initials: O
authors.lastname: Maskri
authors.affiliation: Institut Lavoisier, CNRS, Université de Versailles St. Quentin-en-Yvelines, 45 avenue des Etats-Unis, 78035 Versailles, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Barbier
authors.affiliation: Institut Lavoisier, CNRS, Université de Versailles St. Quentin-en-Yvelines, 45 avenue des Etats-Unis, 78035 Versailles, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: David
authors.affiliation: LBPA, CNRS, Institut d'Alembert, ENS de Cachan, 61 Avenue du P(t) Wilson, F-94235 Cachan, France. Electronic address: philippe.fosse@ens-cachan.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Fossé
authors.affiliation: PPSM, CNRS, Institut d'Alembert, ENS de Cachan, 61 Avenue du P(t) Wilson, F-94235 Cachan, France. Electronic address: joanne.xie@ens-cachan.fr.
authors.forename: Juan
authors.initials: J
authors.lastname: Xie
mesh_terms: D000215:Acylation; D001483:Base Sequence; D015497:HIV-1 / Q000235:genetics / Q000378:metabolism; D016174:Hepacivirus / Q000235:genetics / Q000378:metabolism; D006801:Humans; D006841:Hydrocarbons, Aromatic / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism
chemical_list: D006841:Hydrocarbons, Aromatic; C034477:RNA primers; D012313:RNA
keywords: Active ester; Acyl fluoride; Acylating reagent; RNA; SHAPE chemistry; Symmetric anhydride