title: 1,10-Phenanthroline-copper, a footprinting reagent for single-stranded regions of RNAs.
abstract: The 1,10-phenanthroline-cuprous complex (OP-Cu) with hydrogen peroxide as a coreactant nicks the single-stranded loops and bulges of RNA stem-loop structures more rapidly than the double-stranded stems. This chemical nuclease is therefore a useful footprinting reagent for these regions and can be used to monitor both intramolecular and intermolecular hybridization of single-stranded domains. The formation of A-form structures characteristic of either RNA-RNA or RNA-DNA duplexes inhibits scission because it blocks the binding site of the coordination complex in single-stranded loops and not because the oxidatively sensitive hydrogens of the ribose moiety are blocked. The C-4' and C-1' hydrogens are accessible to solvent in A-structures.
authors.affiliation: Department of Biological Chemistry, School of Medicine, University of California, Los Angeles 90024-1570.
authors.forename: A
authors.initials: A
authors.lastname: Mazumder
authors.forename: C B
authors.initials: CB
authors.lastname: Chen
authors.forename: R
authors.initials: R
authors.lastname: Gaynor
authors.forename: D S
authors.initials: DS
authors.lastname: Sigman
mesh_terms: D001483:Base Sequence; D003300:Copper / Q000737:chemistry; D006861:Hydrogen Peroxide / Q000737:chemistry; D006868:Hydrolysis; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010618:Phenanthrolines / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D016914:Ribonuclease H / Q000494:pharmacology; D013329:Structure-Activity Relationship
chemical_list: D010618:Phenanthrolines; C014741:bis(1,10-phenanthroline)copper(2+) ion; D012313:RNA; D003300:Copper; D006861:Hydrogen Peroxide; D016914:Ribonuclease H