Fig. 3

Cleavage site assembly and proposed catalytic mechanism. a Detailed conformations of the GG-kink and G13 observed in the DNAzyme(2′-OMe-G) structure. b Comparison of the catalytic activities of the wild-type DNAzyme, mutants with methylated G6 or G13, and mutants with G6:C12 replaced with other Watson–Crick base pairs. Due to overlapping with Dz36-AT, the curves for Dz36-CG and Dz36-TA are not visible. c Coordination of Pb²⁺ and the catalytic water observed in the DNAzyme-Pb²⁺ structure. The annealed F_o–F_c omit maps for Pb²⁺ and the water molecule are contoured at 3.0 σ level and colored in green. d Proposed mechanism for the RNA substrate cleavage by 8–17 DNAzyme. The N1 atom of G13 deprotonates the 2′-OH group of the attacking G−1 residue. The O6 atom of G6 coordinates with Pb²⁺, which will activate the catalytic water molecule (general acid) to provide a proton to the O5′ atom of the leaving residue G+1. e Surface representation showing the preformed cation binding cage. The Pb²⁺ is shown as a black sphere. The G−1 and G+1 residues are shown as stick models in yellow. The phosphorus atoms and the oxygen atoms of the backbone phosphate groups of the DNAzyme are colored in orange and red, respectively