Introduction
Throughout our project we have been able to contribute to the iGEM community with biological parts, protocols, custom hardware and software. We hope these contributions will prove useful to subsequent projects.
Our Wet Lab Parts
In all of our detection methods, we developed new biological parts as follows:
| New Basic Parts | Part Name | Link |
|---|---|---|
| BBa_25M7R6HJ | ath-miR399f BRET RCA padlock probe | BBa_25M7R6HJ |
| BBa_25FW084E | ath-miR399f G-quadruplex RCA padlock probe | BBa_25FW084E |
| BBa_2532ENJQ | ath-miR399f sandwich hybridisation mobile probe | BBa_2532ENJQ |
| BBa_25727DQC | ath-miR399f sandwich hybridisation immobilised probe | BBa_25727DQC |
Our Extraction and Detection Kit
We have developed several pieces of hardware for extraction of RNA, and detection of fluorescence. These include a micropestle, hand centrifuge and dark box.
The most notable are the hand centrifuge and dark box. We believe that the hand powered centrifuge poses utility to other iGEM projects, as a cheap alternative to lab equipment, hopefully proving useful in development of field test kits.
The dark box, and corresponding electronics and smartphone app will hopefully be used by other iGEM teams for fluorescence detection (swapping LEDs for the necessary wavelengths). Hopefully this will make some diagnostics and other fluorescence based assays more accessible to more teams worldwide. Unfortunately, while we have not fully developed standardised protocols for the detection kit, we have made all software and 3D files as accessible as possible, such that other teams may build up on this foundation to make fluorescence detection even more accessible to the iGEM community.
Gene Ontology Explorer
To aid in determining candidate miRNAs for diagnosis we developed a software tool that classifies miRNAs by gene ontology and sequence similarity. By using this to determine targets, offsite binding and false positives can be minimised when detecting miRNAs. We have added the capacity to screen various species and filter by different physiological effects, in the hope that further diagnostic projects may also identify the best possible candidate miRNAs.
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