ToeHolder is a tool that can efficiently design toehold riboswitches for the detection of a target gene. A toehold riboswitch is an RNA molecule that contains the necessary elements for the expression of a reporter gene,i.e. a ribosome binding sequence (RBS), a start codon, and the reporter gene sequence. What makes toehold riboswitches special is that they fold into a secondary structure that blocks the access of the ribosome to the RBS, thus preventing gene expression. However, they are carfefully designed so that they can bind to a trigger sequence within a target gene, which results in the unfolding of the secondary structure and allows the expression of the reporter gene (Green et al 2014. Cell). Applications for toehold riboswitches range from detection of sequences of pathogenic organisms (Pardee et al. 2016. Cell; Ma et al. 2018. Synthetic Biology) to creating logical systems (Green et al. 2014. Cell; Green et al. 2017. Nature).
Principle of ToeHold Switch Mechanism.
Download ToeHolder
How it Works
Toeholder aims to facilitate the design of these molecules by offering the following capabilities :
- Testing all the different trigger sequences within a target gene.
- Simulating the secondary structure of the proposed riboswitch for each trigger.
- Simulating the binding of each toehold riboswitch to the target gene to test if it binds accurately to its corresponding trigger.
- Simulating the secondary structure of the proposed riboswitch for each trigger.
- Aligning to user-defined genomes in order to select generalist or specific riboswitches as needed.