Team:UParis BME/Contribution

SwitchMi Designer: a software to design toehold switches targeting microRNA

One of the main goals of our project is to design a set of toehold switches that are functional in detecting cancer miRNAs. None of the tools developed by the former iGEM teams allow the design of toehold switch targeting microRNA. Therefore, we decided to create our own toehold switch design tool, inspired by these previous softwares. This is SwitchMi Designer, the first tool to design a bank of toehold switches targeting microRNAs.

In vitro characterisation of the candidates is required to further improve the SwitchMi Designer and precise the best toehold switch design for microRNA targeting. For future iGEM teams, the source code and explanations are available on GitHub. Our GitHub repository provides an easily accessible source of code that can be used as inspiration for anybody interested in using SwicthMi Designer. They are free to use or modify it to satisfy their needs. Unfortunately, our team was not able to test the toehold switch designed by SwitchMi Designer.

New parts

This year, one of our contributions for future iGEM teams is the introduction of new parts to the iGEM parts registry. These new parts correspond to toehold switch sequences, focusing on the detection of multiple cancer miRNAs. With the right modifications, future teams can use them for the detection of more specific cancers, or for detecting other interesting and useful miRNAs.

For our project, we decided to design toehold switches focusing on the detection of two miRNAs, involved in most cancers: hsa-miRNA-21-5p and hsa-miRNA-141-5p. We designed multiple toehold switch sequences for each of these two miRNAs, thanks to our software SwitchMi Designer. We used several methods to produce these parts and express them into Escherichia coli. Protocols and explanations of these methods are described in our wetlab.

We hope that future teams can benefit from these parts, as a base for their projects, and go further than us in the improvement of these parts to succeed in their project.

Tools for microfluidic chip design and fabrication

During our project, we realised that microfluidics was not a very accessible notion in the iGEM community, when it can be very useful in multiple projects every year. We provide future teams with useful documentation and notions about this fascinating field of science. We also provide 2D and 3D models of our chip, with all the necessary information required to reproduce it. Finally, we give some tips and a quick protocol for teams that want to build their own microfluidic chip. We hope that future iGEM teams that are interested in cancer detection and/or microfluidics design or any applications of this device could use our design as a foundation to build on for their project. Models and explanations are described in our drylab.

iGEMathon & LifeStory : helping future teams in their human practices work

Human practices and Integrated Human Practices is not always an easy work to do in an iGEM project. With iGEMathon/LifeStory, our team wants to help future iGEM teams with this process, by providing a guide, in collaboration with other teams, where several notions around Human Practices are explained, according to the vision of the participating teams. Different stories about the integration of Human Practices into our projects are told. We hope this can be useful for future teams, which can probably be lost when starting their project regarding these abstract notions.

Experiments and protocols available for future teams

Another contribution we want to give to future teams is a precise explanation of all our experiments and protocols. We know how hard it can be for iGEM teams to find the right protocols, especially teams participating in iGEM for the first time. Therefore, we made sure to have all our experiments well explained, with some tips to improve chances of succeeding. Future teams can find generic experiments, such as cell cultures, or plasmid extractions, and more specific experiments to our project. You can find all of the protocols and experiments we performed here.
Furthermore, if you are interested in cancer detection using microfluidics, biofluid exosome extraction, toehold switches or blood miRNA as cancer biomarkers, you can find literature reviews in our science communication page.