The toehold domain (first 15 nucleotides) of the switch RNA is crucial for the binding of the trigger RNA to the switch RNA: this domain must have minimal paired bases in the switch RNA to ensure the successful binding of this domain with the complementary sequence in the trigger RNA, which allows the unwinding of the switch RNA and permits translation of the reporter protein, RFP, to occur. </p>
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The toehold domain (first 15 nucleotides) of the switch RNA is crucial for the binding of the trigger RNA to the switch RNA during the switch-activation process:
this domain must have minimal paired bases in the switch RNA to ensure the successful binding of this domain with the complementary sequence in the trigger RNA, which allows the unwinding of the switch RNA and permits translation of the reporter protein, RFP, to occur. </p>
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Our program can only calculate the minimal free energy structure (MFE) for each target RNA region to reduce calculation workload. In reality, different conformations of RNAs with the same sequence coexist in solution, whose and the concentrations of those populations are determined by their structures and free energy. Therefore, we manually checked the predicted structures and equilibrium concentrations of the ten suboptimal structures of each influenza switches with the lowest MFEs on the web tool developed by ViennaRNA package(http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/barriers.cgi)[2]. Then we predicted the performance of each influenza switches and compared with experimental results.</p>
Our program can only calculate the minimal free energy structure (MFE) for each target RNA region to reduce calculation workload. In reality, different conformations of RNAs with the same sequence coexist in solution, whose and the concentrations of those populations are determined by their structures and free energy. Therefore, we manually checked the predicted structures and equilibrium concentrations of the ten suboptimal structures of each influenza switches with the lowest MFEs on the web tool developed by ViennaRNA package(http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/barriers.cgi)[2]. Then we predicted the performance of each influenza switches and compared with experimental results.</p>