Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme

Abstract

A novel metal-binding site has been identified in the hammerhead ribozyme by ³¹P NMR. The metal-binding site is associated with the A₁₃ phosphate in the catalytic core of the hammerhead ribozyme and is distinct from any previously identified metal-binding sites. ³¹P NMR spectroscopy was used to measure the metal-binding affinity for this site and leads to an apparent dissociation constant of 250–570 μM at 25 °C for binding of a single Mg²⁺ ion. The NMR data also show evidence of a structural change at this site upon metal binding and these results are compared with previous data on metal-induced structural changes in the core of the hammerhead ribozyme. These NMR data were combined with the X-ray structure of the hammerhead ribozyme (Pley HW, Flaherty KM, McKay DB. 1994. Nature 372:68–74) to model RNA ligands involved in binding the metal at this A₁₃ site. In this model, the A₁₃ metal-binding site is structurally similar to the previously identified A₉ metal-binding site and illustrates the symmetrical nature of the tandem G[bull ]A base pairs in domain 2 of the hammerhead ribozyme. These results demonstrate that ³¹P NMR represents an important method for both identification and characterization of metal-binding sites in nucleic acids.