Probing Metal Binding in the 8-17 DNAzyme by TbIII Luminescence Spectroscopy

Metal‐dependent cleavage activities of the 8–17 DNAzyme were found to be inhibited by TbIII ions, and the apparent inhibition constant in the presence of 100 μM of ZnII was measured to be 3.3±0.3 μM. The apparent inhibition constants increased linearly with increasing ZnII concentration, and the inhibition effect could be fully rescued with addition of active metal ions, indicating that TbIII is a competitive inhibitor and that the effect is completely reversible. The sensitized TbIII luminescence at 543 nm was dramatically enhanced when TbIII was added to the DNAzyme–substrate complex. With an inactive DNAzyme in which the GT wobble pair was replaced with a GC Watson–Crick base pair, the luminescence enhancement was slightly decreased. In addition, when the DNAzyme strand was replaced with a complete complementary strand to the substrate, no significant luminescence enhancement was observed. These observations suggest that TbIII may bind to an unpaired region of the DNAzyme, with the GT wobble pair playing a role. Luminescence lifetime measurements in D2O and H2O suggested that TbIII bound to DNAzyme is coordinated by 6.7±0.2 water molecules and two or three functional groups from the DNAzyme. Divalent metal ions competed for the TbIII binding site(s) in the order CoII>ZnII>MnII>PbII>CaII≈MgII. This order closely follows the order of DNAzyme activity, with the exception of PbII. These results indicate that PbII, the most active metal ion, competes for TbIII binding differently from other metal ions such as ZnII, suggesting that PbII may bind to a different site from that for the other metal ions including ZnII and TbIII. Different sites: Metal‐dependent cleavage activities of the 8–17 DNAzyme were found to be inhibited by TbIII ions in a reversible competition mode. Sensitized TbIII luminescence spectral results suggest that TbIII may bind to an unpaired region of the DNAzyme through an inner‐sphere interaction with the GT wobble pair playing a role. Divalent metal ions competed for the TbIII binding site(s) in the order CoII>ZnII>MnII>PbII> CaII≈MgII.