Physicochemical analysis of the interaction between a metal ion and the metal-ion-binding motif in hammerhead ribozymes.

Hammerhead ribozymes have a metal-ion-binding motif in the conserved core region, and this motif can capture several kinds of metal ions. In order to determine what kind of metal ions can be recognized by the motif, we measured 2D 1H-1H NOESY spectra in the presence of various metal ions, such as Cd2+, Na+ and Co(NH3)6(3+) ions, as well as in the absence of these ions. We have completed the assignment of the resonances of the base protons and anomeric protons in all cases, and determined their chemical shift perturbations.