Peters, Gert Maertens, Jo Lammertyn, Jeroen Mey, Marjan De Exploring of the feature space of <i>de novo</i> developed post-transcriptional riboregulators - Fig 1 <p>A) Schematic overview of the translation inhibiting RNA (tiRNA) working mechanism B) Workflow for the <i>in silico</i> 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) <i>In vivo</i> 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)<sub>corrected</sub> = (FP-FP<sub>bg</sub>)/(OD-OD<sub>bg</sub>) with FP<sub>bg</sub> = fluorescence of the strain without fluorescent protein expression and OD<sub>bg</sub> = 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.</p> gene repression;gene expression modulation;squares regression model;target untranslated regions;protein expression levels;RNA;translation initiation modulation;post-transcriptional riboregulators Metabolic engineering 2018-08-17
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10.1371/journal.pcbi.1006170.g001