I would like to amplify whole genome DNA but also tag it with a 40 bp sequence that can crossover with the chromosome of a naturally competent bacterium. The point is to use random WGA to amplify large tracts of DNA from a bacterium with an unusual catabolic activity. The idea is to clone the operon needed for this catabolic activity using a gain of function selection in the naturally competent bacterium. The idea was that the 40mer would allow for crossing over with the recipient chromosome, but the random hexamer at the 3' end would allow the phi29 polymerase to begin polymerization at a variety of places.

I'm using the NEB enzyme & their reaction conditions.

I'm getting no amplification whatsoever. We see massive amounts of unincorporated primer on the gel, and nothing else.

I don't have anybody in the city to talk to about the technical details, so any advice would be greatly appreciated.

Thanks.