Figure 4

A sample structure configuration depicting a partial conformation of the binary logic XOR operation. A sample structure configuration depicting a partial conformation of the binary logic XOR operation, where the presence of two effectors yield no activation of the molecule (cf. XOR in Table 2). The crinkled lines in the figure represent the helix II base pairing of the active hammerhead ribozyme, while the bold wavy line represent conserved region (CUGAUGAG). The small dashed-lines denote un-fixed conformation, where the base position belonging to this region can be either paired or unpaired as long as other mandatory regions (i.e., the base pairing of CUGAUGAG-region and the complementary half of the helix II, effector 1 (E1) with its binding site and effector 2 (E2) with its binding site) are present.