Visualizing metal-ion-binding sites in group I introns by iron(II)-mediated Fenton reactions.
BACKGROUND
Most catalytic RNAs depend on divalent metal ions for folding and catalysis. A thorough structure-function analysis of catalytic RNA therefore requires the identification of the metal-ion-binding sites. Here, we probed the binding sites using Fenton chemistry, which makes use of the ability of Fe2+ to functionally or structurally replace Mg2+ at ion-binding sites and to generate short-lived and highly reactive hydroxyl radicals that can cleave nucleic acid and protein backbones in spatial proximity of these ion-binding sites.


RESULTS
Incubation of group I intron RNA with Fe2+, sodium ascorbate and hydrogen peroxide yields distinctly cleaved regions that occur only in the correctly folded RNA in the presence of Mg2+ and can be competed by additional Mg2+, suggesting that Fe2+ and Mg2+ interact with the same sites. Cleaved regions in the catalytic core are conserved for three different group I introns, and there is good correlation between metal-ion-binding sites determined using our method and those determined using other techniques. In a model of the T4 phage-derived td intron, cleaved regions separated in the secondary structure come together in three-dimensional space to form several metal-ion-binding pockets.


CONCLUSIONS
In contrast to structural probing with Fe2+/EDTA, cleavage with Fe2+ detects metal-ion-binding sites located primarily in the inside of the RNA. Essentially all metal-ion-binding pockets detected are formed by tertiary structure elements. Using this method, we confirmed proposed metal-ion-binding sites and identified new ones in group I intron RNAs. This approach should allow the localization of metal-ion-binding sites in RNAs of interest.
Berens
C
C
Lehrstuhl für Mikrobiologie, Institut für Mikrobiologie, Universität Erlangen-Nürnberg, Germany. berens@gem.univie.ac.at
Streicher
B
B
Schroeder
R
R
Hillen
W
W
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D002413:Cations, Divalent; D018360:Crystallography, X-Ray; D005296:Ferrous Compounds / Q000737:chemistry*; D006868:Hydrolysis; D007438:Introns; D008670:Metals / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism*; D016053:RNA, Protozoan / Q000737:chemistry / Q000378:metabolism*; D012264:Ribonucleotide Reductases / Q000235:genetics
D002413:Cations, Divalent; D005296:Ferrous Compounds; D008670:Metals; D016337:RNA, Catalytic; D016053:RNA, Protozoan; D012264:Ribonucleotide Reductases; C101141:anaerobic ribonucleotide reductase