Figure 3.

Identification of a triplex interaction between substrate and catalyst DNAs. A revised structural representation portrays a triple-helix interaction (dots) between the four base pairs of stem II and four consecutive pyrimidine residues near the 5′ end of the substrate DNA. c4 and s4 represent sequence variants of c3 and s3 that retain base pairing within stem II and that use an alternate sequence of base triples. DNA cleavage assays were conducted as described in Fig. 2A. Bracket identifies the position of the substrate cleavage products.