<h3>In silico design of Influenza Toehold switches</h3>
<h3>In silico design of Influenza Toehold switches</h3>
−
According to Green et al., the optimal length of RNA to be detected by a toehold switch is around 30 bp. In other words, a target RNA with 1000 bp in length will give 970 possible switches. However, the performances of each possible switch are different, since the performance is governed by serval parameters in the target region, such as the minimum free energy (For more information, please visit <a href="https://2017.igem.org/Team:Hong_Kong-CUHK/Model">RNA thermodynamics modelling page</a>). To minimize the manpower on screening of the switches, we constructed an online toehold switch design program. Apart from basic thermodynamic parameters, it also screens for rare codon, stop codon and RFC illegal sites along the sequence. In addition, the built- in BLAST function also automatically screen for nonspecific region to avoid false positive detection. Ultimately, the program can sort a list of “best” Toehold Switch sequence according to their free energy using the embedded function of <a href="https://www.tbi.univie.ac.at/RNA/">“Vienna RNA”</a> (8). The program facilitates the construction of toehold switch by providing a user-friendly interface with novel screening function.
+
According to Green et al., the optimal length of RNA to be detected by a toehold switch is around 30 bp. In other words, a target RNA with 1000 bp in length will give 970 possible switches. However, the performances of each possible switch are different, since the performance is governed by serval parameters in the target region, such as the minimum free energy (For more information, please visit <a href="https://2017.igem.org/Team:Hong_Kong-CUHK/Model">RNA thermodynamics modelling page</a>). To minimize the manpower on screening of the switches, we constructed an <a href="https://2017.igem.org/Team:Hong_Kong-CUHK/Software"> online toehold switch design program </a>. Apart from basic thermodynamic parameters, it also screens for rare codon, stop codon and RFC illegal sites along the sequence. In addition, the built- in BLAST function also automatically screen for nonspecific region to avoid false positive detection. Ultimately, the program can sort a list of “best” Toehold Switch sequence according to their free energy using the embedded function of <a href="https://www.tbi.univie.ac.at/RNA/">“Vienna RNA”</a> (8). The program facilitates the construction of toehold switch by providing a user-friendly interface with novel screening function.