Targeting

The BioBytes team has chosen to use a recombination system from bacteriophage lambda. Lambda Red recombinase specifically recombines on the ends of a linear fragment of DNA. If the ends of this fragment are homologous to two separate sites on the E. coli chomosome, the genetic material between these two homologous regions will be exchanged. This will be the basis for our targeting system.

The homologous regions must be a minimum of 50 base pairs in length for recombination to occur at a significant frequency. This can be achieved in different ways:

First 5' extensions corresponding to the homologous sequence can be added to any gene using PCR amplification. This would allow a PCR product to be targeted to a specific site for insertion. Because our constructs will be recircularized and grown (see DNA assembly), this would require us to PCR each plasmid construct seperately in order to add the homologous regions to the ends.

An alternative is to use the genes on either end of our construct as the homologous regions. As an example, we could first locate a region of genes which were deemed inessential through literature review and our Matlab modelling. This region would necessarily be flanked by an essential gene at either end. We would then assemble a plasmid containing these two essential genes. If the insertion is successful, we would be left with a chromosome without this region of inessential genes: