title: Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex.
abstract: Oxidation of RNA can be effected by two different techniques: a photochemical, electron-transfer method termed "flash-quench" and direct oxidation by metal oxo complexes. The flash-quench method produces selective oxidation using a metal photosensitizer, tris(bipyridyl)ruthenium(III) trichloride (Ru(bpy)(3)(3+)), and quencher, pentaamminechlorocobalt(III) chloride (Co(NH(3))(5)Cl(2+)). We have optimized the flash-quench technique for the following RNAs: tRNA(Phe), human ferritin iron-responsive element (IRE), and a mutated human ferritin IRE. We have also employed a chemical footprinting technique involving the oxoruthenium(IV) complex (Ru(tpy)(bpy)O(2+) (tpy = 2,2',2''-terpyridine; bpy = 2,2'-bipyridine)) to oxidize guanine. Comparison of the two methods shows that the flash-quench technique provides a visualization of nucleotide accessibility for a static conformation of RNA while the Ru(tpy)(bpy)O(2+) complex selectively oxidizes labile guanines and gives a visualization of a composite of multiple conformations of the RNA structure.
authors.affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
authors.forename: Dana R
authors.initials: DR
authors.lastname: Holcomb
authors.forename: Patricia A
authors.initials: PA
authors.lastname: Ropp
authors.forename: Elizabeth C
authors.initials: EC
authors.lastname: Theil
authors.forename: H Holden
authors.initials: HH
authors.lastname: Thorp
mesh_terms: D003035:Cobalt / Q000737:chemistry; D004579:Electron Transport; D005293:Ferritins / Q000235:genetics; D006147:Guanine / Q000737:chemistry*; D006801:Humans; D009690:Nucleic Acid Conformation; D009942:Organometallic Compounds / Q000737:chemistry*; D010084:Oxidation-Reduction; D010100:Oxygen / Q000737:chemistry*; D010777:Photochemistry; D012313:RNA / Q000737:chemistry*; D020218:Response Elements / Q000235:genetics; D012428:Ruthenium / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D009942:Organometallic Compounds; D003035:Cobalt; D006147:Guanine; D012313:RNA; D012428:Ruthenium; D005293:Ferritins; D010100:Oxygen