Team:British Columbia/Project

From 2009.igem.org

Traffic Light Overview

Depending on the concentration of a particular substrate in the medium, E. coli will respond accordingly by producing different coloured fluorescence proteins. A diagram would look like this:

The E. coli Traffic Light Biosensor is composed of three major subparts: variable arabinose-inducible promoters, RNA lock and key system, and reverse antisense promoters for input detection, color activation and traffic light switching respectively.

Here is what's happening inside our traffic light:

Schematic black-box representation of the E. coli Biosensor that detects various concentration inputs and color outputs. The idea is discrete analog outputs based on a user-specified threshold for each range of concentration.

For our ideas to work, we will need:
1. A variable sensitivity biosensor
2. A lock-and-key logic gate system]
3. An antisense "off" switch

Tools used and produced

To assist our project, we produced a Biobrick digestion engine and Biobrick picture maker to help out the project:

http://www.pkts.ca/bb - Biobrick digestion engine - enter the name of a biobrick plasmid and biobrick insert, and this will show you the product of an EcoRI and PstI digestion/ligation as a FASTA file (suitable for viewing in your favorite program).

http://www.pkts.ca/brickedit/ - Biobrick picture maker - enter a sequence of letters corresponding to the icons, and the program will produce a concatenated file of the Biobrick.

Also, we generated a handy Fasta file containing every biobrick from [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=List Here]:

Biobricks.zip - Fasta file containing every biobrick

We also found the following tools very helpful:

http://rna.tbi.univie.ac.at/ - a package of prediction tools for RNA structures; we used RNAfold to annotate the key and lock structures

http://mobyle.pasteur.fr/cgi-bin/portal.py - a set of web-accessible bioinformatics tools including Mfold, which determines 2D RNA structure and draws it

http://frodo.wi.mit.edu/ - Primer3, a primer design program