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Fig. 8 | BMC Bioinformatics

Fig. 8

From: Multi-objective optimization for RNA design with multiple target secondary structures

Fig. 8

A design example of ribozyme-based RNA device. Gray circles indicate sequence constraints. The original ribozyme consensus sequence motifs and loop nucleotides of L2bulge1 [15] were used as sequence constraints. The structures and free energies shown in this figure were computed by Fold in RNAstructure package. a Ribozyme-active conformation predicted as the MFE structure. b Ribozyme-inactive conformation predicted as the MFE structure when the aptamer domain structure is constrained; the region ranging from 43 to 72 nt is the theophylline aptamer domain. The designed sequence is GCUGUCUCUCUCUGUGCUUGAGGGACUGAUGAGAGUGUACCAAUACCAGCAUCGUCUUGAUGCCCUUGGCAGU GGUAUGGUGAAUUCGAAACAGC. These structures were visualized by VARNA [40]

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