作者: Gesine Domin , Sven Findeiß , Manja Wachsmuth , Sebastian Will , Peter F. Stadler
DOI: 10.1093/NAR/GKW1267
关键词: Computational biology 、 Protein secondary structure 、 RNA 、 In silico 、 Riboswitch 、 Biology 、 Synthetic biology 、 Aptamer 、 Minimal free energy 、 Computational design
摘要: Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells sense and respond exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach the design of theophylline based on secondary structure prediction. These been constructed regulate ligand-dependent transcription termination in Escherichia coli. Here, we test usability this strategy by applying tetracycline streptomycin aptamers. The resulting exhibit robust regulatory properties vivo. Tandem fusions these with represent logic gates responding two different input signals. contrast, aptamer appears be Investigations underlying revealed differences between silico prediction probing. conclude only adopting minimal free energy (MFE) are suitable targets construction equilibrium thermodynamics structures. Further improvements required implement structures not corresponding calculated MFE state.