Unit

UNIT 6.8 Probing RNA Structure and Metal-Binding Sites Using Terbium(III) Footprinting

  1. Dinari A. Harris,
  2. Nils G. Walter

Published Online: 1 AUG 2003

DOI: 10.1002/0471142700.nc0608s13

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Harris, D. A. and Walter, N. G. 2003. Probing RNA Structure and Metal-Binding Sites Using Terbium(III) Footprinting. Current Protocols in Nucleic Acid Chemistry. 13:6.8:6.8.1–6.8.8.

Author Information

  1. University of Michigan, Ann Arbor, Michigan

Publication History

  1. Published Online: 1 AUG 2003
  2. Published Print: JUN 2003

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.

Keywords:

  • catalytic RNA;
  • lanthanide ion;
  • metal probing;
  • RNA structure probing;
  • sequencing