Probing RNA structure and metal-binding sites using terbium(III) footprinting.
The function of an RNA molecule is determined by its overall secondary and tertiary structure. The tertiary structure is facilitated and stabilized by the interaction with metal ions. The current chapter offers a detailed protocol on the use of the lanthanide metal ion terbium(III) as a powerful probe of RNA structure and metal-binding properties. When incubating RNA with low (micromolar) concentrations of terbium(III), specific backbone scission by partially deprotonated aqueous terbium(III) complexes can be used to detect high-affinity metal-binding sites, while incubation with high (millimolar) terbium(III) concentrations cleaves the RNA backbone preferentially at structurally accessible regions, providing a footprint of the RNA secondary and tertiary structure.
Harris
Dinari A
DA
University of Michigan, Ann Arbor, Michigan, USA.
Walter
Nils G
NG
D001483:Base Sequence; D001665:Binding Sites; D008670:Metals / Q000378:metabolism*; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D015347:RNA Probes / Q000737:chemistry; D011868:Radioisotopes / Q000494:pharmacology; D017423:Sequence Analysis, RNA / Q000379:methods*; D013725:Terbium / Q000494:pharmacology*
D008670:Metals; D015347:RNA Probes; D011868:Radioisotopes; D013725:Terbium; D012313:RNA