title: Osmium tetroxide as a probe of RNA structure.
abstract: Structured RNAs have a central role in cellular function. The capability of structured RNAs to adopt fixed architectural structures or undergo dynamic conformational changes contributes to their diverse role in the regulation of gene expression. Although numerous biophysical and biochemical tools have been developed to study structured RNAs, there is a continuing need for the development of new methods for the investigation of RNA structures, especially methods that allow RNA structure to be studied in solution close to its native cellular conditions. Here we use osmium tetroxide (OsO4) as a chemical probe of RNA structure. In this method, we have used fluorescence-based sequencing technologies to detect OsO4modified RNA. We characterized the requirements for OsO4modification of RNA by investigating three known structured RNAs: the M-box, glycine riboswitch RNAs, and tRNAaspOur results show that OsO4predominantly modifies RNA at uracils that are conformationally exposed on the surface of the RNA. We also show that changes in OsO4reactivity at flexible positions in the RNA correlate with ligand-driven conformational changes in the RNA structure. Osmium tetroxide modification of RNA will provide insights into the structural features of RNAs that are relevant to their underlying biological functions.
authors.affiliation: Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China.|Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.|Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
authors.forename: Danbin
authors.initials: D
authors.lastname: Li
authors.affiliation: Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China.|Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.|Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
authors.forename: Dongrong
authors.initials: D
authors.lastname: Chen
authors.affiliation: Fudan University Pudong Medical Center, Pudong, Shanghai 201399, China.|Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.|Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China.
authors.forename: Alastair I H
authors.initials: AI
authors.lastname: Murchie
mesh_terms: D001483:Base Sequence; D015335:Molecular Probes / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009993:Osmium Tetroxide / Q000737:chemistry*; D012349:RNA, Transfer, Asp / Q000737:chemistry* / Q000235:genetics; D058928:Riboswitch / Q000235:genetics*; D013194:Staining and Labeling / Q000379:methods; D014498:Uracil / Q000737:chemistry
chemical_list: D015335:Molecular Probes; D012349:RNA, Transfer, Asp; D058928:Riboswitch; D014498:Uracil; D009993:Osmium Tetroxide
keywords: RNA; RNA structure; chemical probe; osmium tetroxide