Team:British Columbia/Project

From 2009.igem.org

(Difference between revisions)

Revision as of 01:28, 22 October 2009

'Overview of the Traffic Light Biosensor:
A flexible, modular, and transparent system for multi-level assessment of variable inputs.'

Biosensors have a diverse variety of real-world functions, ranging from measuring blood glucose levels in diabetes patients to assessing environmental contamination of trace toxins. The majority of these sensors are highly specific for a single input, and their outputs often require specialized equipment such as surface plasmon resonance chips. Our project aims to create a biosensor that recognizes a specific target and alters its output fluorescence from green, to yellow, to red as a function of concentration up to critical levels (hence, a biological "traffic light").

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.

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.

Subparts:
1. A variable sensitivity biosensor
2. A lock-and-key logic gate system]
3. An antisense "off" switch

Miscellaneous Data

We also produced a couple tools to help out the project:

Biobricks.zip - Fasta file containing every biobrick from [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=List Here]

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.

Links

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

@@ Line 7: / Line 7: @@
 [[Image:E_coli_Traffic_Light_Subprojects.png|center|thumb||400px|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.]]
+[[Image:E_coli_Traffic_Light_Step_by_Step.png|thumb|center|700px|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.]]
 Subparts:<br>