title: RNA structural analysis by enzymatic digestion.
abstract: Enzymatic probing is a rapid, straightforward method for determining which regions of a folded RNA are structurally constrained. It can be carried out using very small amounts of material, and is especially suitable for short RNAs. Here we report a protocol that we have found to be useful and readily adaptable to the evaluation of RNAs up to 150-200 nucleotides in length. Considerations for optimization are also included. In brief, the method includes folding end-labeled RNA into its native conformation, partial digestion with structure-sensitive nucleases, and identification of the cleavage sites by electrophoretic separation of the cleavage fragments.
authors.affiliation: Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.
authors.forename: Elisa
authors.initials: E
authors.lastname: Biondi
authors.forename: Donald H
authors.initials: DH
authors.lastname: Burke
mesh_terms: D000818:Animals; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D004720:Endonucleases / Q000378:metabolism; D006801:Humans; D009690:Nucleic Acid Conformation; D010766:Phosphorylation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D059370:RNA Folding
chemical_list: D012313:RNA; D004720:Endonucleases