Exploring of the feature space of de novo developed post-transcriptional riboregulators - Fig 1
A) Schematic overview of the translation inhibiting RNA (tiRNA) working mechanism B) Workflow for the in silico selection of the tiRNAs comprising the design of experiments (DOE) to unravel design principles. The defined tiRNA features (free energy of the tiRNA monomer (EA), free energy of the tiRNA-tiRNA dimer (EAA), free energy of the tiRNA-UTR dimer (EAB), formation energy of the tiRNA-tiRNA dimer (FAA), formation energy of the tiRNA-UTR dimer (FAB), total seed energy (ETS), intermolecular binding seed energy (EIS), probability availability of UTR (PAU), RBS coverage of length 5 (RBS5), RBS coverage of length 11 (RBS11), paired termini (PT), and the tiRNA length (L)) are calculated for a tiRNA library created based on a specific target 5’ untranslated region (UTR). C) In vivo assessment of the tiRNA in the designed experiment D) Linking features to tiRNA performance through modeling. The fluorescence (FP) per optical density (OD) for a strain was calculated as follows: (FP/OD)corrected = (FP-FPbg)/(OD-ODbg) with FPbg = fluorescence of the strain without fluorescent protein expression and ODbg = OD of the medium. The relative protein expression (%) was defined as the (FP/OD)corrected in presence of the riboregulator divided by the (FP/OD)corrected in the absence of the riboregulator.