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).
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).
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.
Edited by cerqueiragm, 14 June 2011 - 03:29 AM.