Figure 3.

Alternative designs of theophylline-sensing pT181 ncRNA fusions. (A) Screening of eight designed pseudoknot mutants (Supplementary Figure S5) results in theo–P–pT181, which displays strong theophylline-inducible repressive effects on its target. (B) An alternative design of theophylline-sensing pT181 ncRNA fusions based on the strand-exchange strategy by mutating the lower bottom stem region of the ncRNAs. The sequences of the best mutant screened from 15 mutants (Supplementary Figure S6) is shown as theo–SE–pT181 (SE for strand exchange). In vivo fluorescence data from flow cytometry is shown on the bottom. The repression percentage between 3 mM and 0.01 µM theophylline is 83.4%, compared to 86.6% between positive and negative controls. The insets show the cytometry histograms corresponding to three ligand concentrations in both (A) and (B).