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Figure 2 | Genome Biology

Figure 2

From: Searching genomes for ribozymes and riboswitches

Figure 2

The hammerhead ribozymes are based on a three-way junction and there are two main types. (a) Type I has the ends of the single-stranded RNA on stem I; (b) type III has the ends of the single-stranded RNA on stem III. For unknown reasons, potential type II ribozymes (ends of the single-stranded RNA on stem II) have never been observed. The three-dimensional architecture is maintained by coaxial stacking of stems II and III, which, through constraints in the conserved three-way junction residues [92], orients stem I so that loop-loop interactions between stems I and II form (Figure 3) [40,42]. The internal loop of stem II (IL2) is often replaced by a capping loop (CL2); similarly, CL1 in type III can be replaced by an internal loop (IL1) followed by another hairpin. Although only one structure has been fully characterized, sequence alignments show that the loop-loop interactions (mainly constituting non-Watson-Crick pairs) are very diverse.

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