Probing RNA structure and metal-binding sites using terbium(III) footprinting

Current Protocols in Nucleic Acid Chemistry
Dinari A Harris, Nils G Walter

Abstract

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.

References

Apr 20, 1999·Methods : a Companion to Methods in Enzymology·S P Ryder, S A Strobel
Apr 25, 2000·Journal of Molecular Biology·N G WalterJ M Burke
Dec 2, 2000·Nature Structural Biology·R K SigelA M Pyle
Dec 6, 2000·RNA·M R Hargittai, K Musier-Forsyth
Jun 13, 2001·Biochemistry·A Vaidya, H Suga
Aug 31, 2002·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Anna Marie Pyle
Dec 6, 2002·Nucleic Acids Research·Hirohide Saito, Hiroaki Suga

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Citations

Jan 6, 2009·Journal of the American Chemical Society·Matthew J BelousoffBim Graham
Oct 26, 2005·RNA·Meredith Newby LambertNils G Walter
Nov 19, 2013·RNA·Pallavi K Choudhary, Roland K O Sigel

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