Helix-slipping uses a sequence that forms an imperfectly paired double-stranded stem that is flexible in its nucleotide base-pairing through a "slip-structure" mechanism (Win and Smolke, 2007). It does not allow for rational design and results in disruption or restoration of the hammerhead ribozyme in response to changes in the aptamer. Helix-slipping only results in OFF switches due to this lack of rational design. However, it works in much the same way that the ON switch does in strand-displacement because when the ligand binds to the aptamer, the catalytic core is restored and the ribozyme can self-cleave, preventing gene expression (Figure 4A). In addition, because helix-slipping uses random aptamers created by directed evolution, the level of repression can vary from aptamer to aptamer (Figure 4B).
Figure 4. "Regulatory properties of the helix-slipping information transmission mechanism. The color scheme corresponds to that used in Fig. 1 with the following exception: communication module sequence, orange. (A) Gene expression OFF ribozyme switch platform based on helix slipping, L2cm4. The base stem of the aptamer was replaced with a communication module. (B) Regulatory activities of helix-slipping-based ribozyme switches. Gene-regulatory effects of the OFF switches at 5 mM theophylline are reported in fold repression relative to expression levels in the absence of effector. The corresponding communication module sequences are indicated. Gene expression levels are reported as described in Fig. 2." (Win and Smolke, 2007). Image Permission Pending.