Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme

The solution structure of an RNA hairpin modelling the P5 helix of a group I intron, complexed with Co(NH3)(6)(3+), has been determined by nuclear magnetic resonance. Co(NH3)(6)(3+), which possesses a geometry very close to Mg(H2O)(6)(2+), was used to identify and characterize a Mg2+ binding site in the RNA. Strong and positive intermolecular nuclear Overhauser effect (NOE) cross-peaks define a specific complex in which the Co(NH3)(6)(3+) molecule is in the major groove of tandem G.U basepairs. The structure of the RNA is characterized by a very low twist angle between the two G.U base-pairs, providing a flat and narrowed major groove. The Co(NH3)(6)(3+), although highly localized, is free to rotate to hydrogen bond in several ways to the O4 atoms of the uracil bases and to N7 and O6 of the guanine bases. Negative and small NOE cross-peaks to other protons in the sequence reveal a non-specific or delocalized interaction, characterized by a high mobility of the cobalt ion. Mn2+ titrations of P5 show specific broadening of protons of the G.U basepairs that form the metal ion binding site, in agreement with the NOE data from Co(NH3)(6)(3+). Binding constants for the interaction of Co(NH3)(6)(3+) and of Mg2+ to P5 were determined by monitoring imino proton chemical shifts during titration of the RNA with the metal ions. Dissociation constants are on the order of 0.1 mM for Co(NH3)(6)(3+) and 1 mM for Mg2+. Binding studies were done on mutants with sequences corresponding to the three orientations of tandem G.U base-pairs. The affinities of Co(NH3)(6)(3+) and Mg2+ for the tandem G.U base-pairs depend strongly on their sequences; the differences can be understood in terms of the different structures of the corresponding metal ion-RNA complexes. Substitution of G.C or A.U for G.U pairs also affected the binding, as expected. These structural and thermodynamic results provide systematic new information about major groove metal ion binding in RNA. (C) 1999 Academic Press.