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Trouble to UNDERSTAND gene replacement results - (Jun/14/2011 )

Hi everyone,
today I come across with some trouble to UNDERSTAND some gene replacement results.

I've been trying to obtain a knock out bacterial mutant by replacing my gene of interest for a KmR cassette, ok!?. The difference is that I have constructed a linear cassette, which contains the KmR cassette flanked by regions homologous to the flanks of the native gene to be replaced (Flank1 - KmR - Flank2).

I've then transformed the bacterial strain using the linear cassette and obtained Km resistant colonies. Then I've patched them to certify that they are really Km resistant. After this I PCR them using the following primers: Flank 1 forward and Flank 2 reverse (the same used to construct the cassette).

PCR Results:
1. No DNA rxn - No amplification
2. Wild-type rxn - 4 kb band
3. Cassette control rxn - 2 kb band
4. Colony 1 rxn - two bands (4 and 2 kb)
5. Colony 2 rxn - one band (2 kb).

My doubts:
1. Colony 1 could correspond to a single cross-over mutant?
2. Colony 2 could correspond to a gene replaced (knock out) mutant?
3. I've propagated the colony 2 for two more times after initial obtaining. For transformation I've used 10 micrograms of my LINEAR cassette. There is the possibility that the low 2 kb band be due to traces of the linear cassette or you guys think it could be really a double cross over mutant?
3. Someone knows a link to a schematic of a single crossover event using a LINEAR cassette? I tryed everywhere but couldn't find a scheme or diagram.

People, thank you very much for your help.
Kind regards.


Hi cerqueirgm,

I guess both are mutants, but the mutation in first colony possibly still incomplete, in 'merodiploid' stage...(if you doing h.recombination) to make sure what is happening u need to send for sequencing...blast and you will know what gene was amplified...but i think it's better to choose 2nd colony for next stage...that's what i think :)