Lanthanide probes for a phosphodiester-cleaving, lead-dependent, DNAzyme

Abstract

Lanthanides are useful probes for studying metal ion interactions in biological systems. The trivalent cations of the lanthanide metals are unique in that their ionic radii and the first p K a values of bound water molecules vary monotonically along the period. In addition, the europium and terbium cations have the useful property that their luminescence is enhanced when bound to nucleic acids. We have found that lanthanide ions can function as effective co-factors for a lead-dependent, phosphodiester-cleaving catalytic DNA (DNAzyme). We used the unique properties of the lanthanide co-factors to study the metal binding site as well as the catalytic mechanism of the DNAzyme. The catalyzed lanthanide-mediated cleavage occured at neutral pH and at room temperature, with multiple turnovers of substrate. A range of lanthanide ions could act as co-factors, but differently, with the smaller lanthanides (Tb, Tm, Lu) being the most effective. The rate of cleavage of the phosphodiester did not vary linearly with either the ionic radius of the first p K a of lanthanide-coordinated water molecules. The DNAzyme appeared to use only a single bound lanthanide ion as co-factor. Luminescence spectroscopy with terbium revealed the importance of the 2′ hydroxyl group at the cleavage site in lanthanide ion binding, and the substrate molecule alone appeared to generate substantially the catalytically relevant metal-binding site. This model system demonstrated further the utility of complexing lanthanide ions directly to DNA molecules for catalytic purposes. The use of lanthanide ions also provides a means for investigating the metal ion binding sites of nucleic acid enzymes in general.