title: SHAPE analysis of small RNAs and riboswitches.
abstract: We describe structural analysis of small RNAs by SHAPE chemical probing. RNAs are treated with 1-methyl-7-nitroisatoic anhydride, a reagent that detects local nucleotide flexibility; and N-methylisatoic anhydride and 1-methyl-6-nitroisatoic anhydride, reagents which together detect higher-order and noncanonical interactions. Chemical adducts are quantified as stops during reverse transcriptase-mediated primer extension. Probing information can be used to infer conformational changes and ligand binding and to develop highly accurate models of RNA secondary structures.
authors.affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA.
authors.forename: Greggory M
authors.initials: GM
authors.lastname: Rice
authors.affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Busan
authors.affiliation: Department of Computer Engineering, Yildiz Technical University, Istanbul, Turkey.
authors.forename: Fethullah
authors.initials: F
authors.lastname: Karabiber
authors.affiliation: Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, USA. Electronic address: favorov@bme.unc.edu.
authors.forename: Oleg V
authors.initials: OV
authors.lastname: Favorov
authors.affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA. Electronic address: weeks@unc.edu.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Weeks
mesh_terms: D000812:Anhydrides / Q000737:chemistry; D001483:Base Sequence; D019075:Electrophoresis, Capillary / Q000379:methods*; D007202:Indicators and Reagents; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010078:Oxazines / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D058928:Riboswitch; D062367:ortho-Aminobenzoates / Q000737:chemistry
chemical_list: C585663:1-methyl-7-nitroisatoic anhydride; D000812:Anhydrides; D007202:Indicators and Reagents; D010078:Oxazines; D058928:Riboswitch; D062367:ortho-Aminobenzoates; C077537:N-methylisatoic anhydride; D012313:RNA
keywords: Capillary electrophoresis; QuSHAPE; RNA structure; Riboswitch; SHAPE