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Phage sequences in bacterial genomes
Spreading the tools of death
Catching phage recombination in the act
Infectious phage are presumably recombinants that have regained a functional tail fiber gene from one of the CPs. Your goal is to design primers for PCR that will distinguish between the wild type L0121 tail fiber gene and the CP tail fiber genes and allow you to demonstrate that the phages isolated in this way are in fact recombinants.
Since recombination might take place between L0121 and any of the CP tail fiber genes, it would be convenient to find a 5' primer that matched all of the CP genes but not 933W. Likewise, it would be nice to find a 3' primer that matched 933W but not any of the cryptic phage. In short, you want primers that will amplify all possible recombinant phage and only recombinant phage.
How do you find primers that will fit the bill?
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