Fig. 1

Global architecture of the 8–17 DNAzyme. a 8–17 consensus sequence and the predicted secondary structure. The sequence was adapted from the commonly observed sequence variations and mutagenesis experiments. b Sequence and the observed secondary structure of DNAzyme (Dz36) and the substrate (or analog) utilized in the structural and the catalytic cleavage studies. c Cartoon representation showing the overall fold of the DNAzyme/substrate analog complex, based on the high-resolution DNAzyme-Pb²⁺ structure. AsfvPolX proteins, which were utilized to facilitate the crystallization, are colored in light blue or cyan. d The relative arrangement of P1, P2, GG-kink, and the catalytic core. e Close-up view showing the detailed base pairing of the P4 duplex. In c–e, P1, P2, and GG-kink are colored in white, yellow, and magenta, respectively. The sugar puckers and nucleobases of P3 and P4 duplexes are colored in blue and red, respectively, whereas the backbone of P3 and P4 and all other residues are colored in green