Sauer:Plasmid-born λRed recombineering using dsDNA
This protocol was taken (with minor modifications) from Thomason et. al. Current Protocols in Molecular Biology (2007) 1.16.1-1.16.24
Using short (35-40 bp) regions of homology, bacteriophage-encoded recombination machinery allows for the efficient insertion or deletions in gram-negative bacterial chromosomes without regard to restriction sites. The Court lab has extended the "Wanner" method by placing the plasmid-born bacteriophage recombination functions under the control of a temperature sensitive allele lambda repressor (cI857). At low temperatures (30-34 C) the downstream genes are tightly repressed however following a temperature shift to 42 C, these genes are expressed at high levels from the lambda pL promoter. Following induction of the recombination functions, transformed dsDNA is efficiently recombined into the chromosome and recombinants identified by either selection or PCR based screening. Some of the Court lab plasmids carry a temperature sensitive origin allowing for facile plasmid curing by simply shifting to the non-permissive temperature (37) and omitting the selection marker (chloramphenicol in the case of pSIM5).
Primer Design: 5' to 3': 40 nt of homology targeting the chromosomal region of interest 20 nt which bind the the cassette to be amplified (i've often use the b.b. prefix ans suffix for this region allowing me to knock in a variety of constructs to the same chromosomal locus)
PCR: Due to the size of the primers i typically anneal at 57-60 although when this is problematic I will included 2 rounds with lower annealing tempatures at the beginning of the reaction. ex: 92