Team:British Columbia/Project

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

Biosensors have a wide variety of uses, from measuring blood glucose levels in diabetes patients to assessing environmental contamination by 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 given target and shifts its output fluorescence from green, to yellow, to red as concentrations approach critical levels (hence, a biological "traffic light").

Subparts:
1. A variable sensitivity biosensor
2. A lock-and-key logic gate system

Biosensor

Using data derived from random mutagenesis of the pBAD promoter binding sites (5), we intend to construct a library of varying strength pBAD promoters coupled to a reporter gene.

pBAD mutagenesis roadmap

The Experiments

Mutagenesis of pBAD promoter sequence.
Quantification of mutant promoter-driven RFP fluorescence.
BioBrick design and submission.

Results

Qualitative examination of RFP development following arabinose addition found that the weak promoter does, as expected, turn red at a significantly slower rate than the wild type promoter. However, the purported strong promoter is both slower to develop colour as well as reaching a lower maximum intensity. We are currently establishing methods for quantification and modeling of RFP induction by arabinose.

Logic Gates

In 2004, Isaacs et al. (4) constructed a lock and key system termed the riboregulator. Briefly, the riboregulator consists of a lock sequence immediately 5' of and complementary to the RBS; upon transcription, the lock binds to the RBS and prevents translation of the mRNA. This binding can be "unlocked" by the introduction of a "key" mRNA, which disrupts the binding between the lock and RBS and allows translation to resume.

We intend to convert the lock and key as described by Isaacs et al. into standardized BioBrick parts and integrate them with our library of variable strength promoters in order to create a multi-level logic gate system. We also hope to design an additional component, termed the "jammer", which prevents the key from unlocking the lock.

Lock and Key

The lock is a short DNA segment that is the reverse-complement of the lock.

Jammer

Our analog biosensor requires a component to turn off designed lights (i.e. reporter genes) when the target passes a certain threshold. To do so, we have designed a modular, endogenous RNA knockdown system using antisense RNA hybridization. We have independently conceived of using a reverse promoter, that was first described by O’Connor and Timmis (1987), to generate an antisense transcript that hybridizes to the sense transcript, to reduce gene expression.

This is accomplished at the RNA-level through both transcription and translation interfaces. First, when the reverse promoter recruits RNA polymerases, they transcribe in the antisense direction. This causes the sense and anti-sense oriented polymerases to collide, thus reducing transcription (Ward and Murray, 1979; Crampton et al. 2006).

Roadmap

As of the 2009 Jamboree, not all aspects of our project have been completed. Looking forward, we intend to complete, test, and characterize our lock, key and jammer. Once this is done we intend to do the same for a second set of lock, key and jammer that have different sequences and will therefore not interfere with the first set. This second set will be configured to detect a second molecule, distinct from the first. When this is completed, we will try adding logic gates, allowing us to address nine different combinations: high, medium and low concentrations of arabinose combined with high, medium and low concentrations of whatever we choose as our second molecule, possibly an antibiotic. When plated on media with two perpendicular gradients, we should be able to independently control each square of a 3x3 grid, possibly displaying 9 different colors of fluorescent proteins, or generating other metabolites, such as indigo.

Miscellaneous Data

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

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 ==Roadmap==
+As of the 2009 Jamboree, not all aspects of our project have been completed.  Looking forward, we intend to complete, test, and characterize our lock, key and jammer.  Once this is done we intend to do the same for a second set of lock, key and jammer that have different sequences and will therefore not interfere with the first set.  This second set will be configured to detect a second molecule, distinct from the first.  When this is completed, we will try adding logic gates, allowing us to address nine different combinations: high, medium and low concentrations of arabinose combined with high, medium and low concentrations of whatever we choose as our second molecule, possibly an antibiotic.  When plated on media with two perpendicular gradients, we should be able to independently control each square of a 3x3 grid, possibly displaying 9 different colors of fluorescent proteins, or generating other metabolites, such as indigo.
 == Miscellaneous Data ==