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Figure 3 Gallery of RNA-cleaving deoxyribozymes identified by in vitro selection. Most of these deoxyribozymes function in the intermolecular format for in trans cleavage of an RNA linkage. Thick lines and lowercase letters denote RNA; thin lines and uppercase letters denote DNA, and the green arrow marks the cleavage site. The DNA enzyme regions are green; DNA nucleotides involved in Watson–Crick base pairing are brown; nucleotides of the substrate to the 5'-side of the cleavage site are red; and nucleotides to the 3'-side are blue. For clarity, not all nucleotides are shown explicitly, but this does not necessarily imply a lack of sequence requirements. In panel D, the 8–17 deoxyribozyme is shown with the RNA cleavage site requirement a
g. However, the closely related 17E deoxyribozyme (32) can cleave ng (although ag and gg are preferred). Furthermore, a comprehensive study showed that 8–17 variants can be identified that collectively cleave almost any RNA dinucleotide linkage (36). In panel H, the letters F and Q denote a fluorophore and quencher that are separated upon cleavage by the signaling deoxyribozyme.
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