I found out that Nat or Kan selection does not work on drop out plates. The ammonium sulfate interferes with drug selection. I have read that using proline or glycine instead of ammonium sulfate can solve the problem but this hasn't worked for me either. A colleague told me pH'ing the media to about 7 will work. My yeast strain has a URA3 plasmid and is marked with genomic NatMX / KanMX cassette. thanks!
You can use drop out media but you have to use monosodium glutamate instead of ammonium sulfate at a final concentration of 1 mg/ml (I am assuming your talking about plates containing G418 not kanamycin). However, If you are selecting for the plasmid alone it is not absolutely necessary to select for chromosomally integrated resistance as that should be stable (unless you suspect your strain is contaminated with a non-resistant strain) and you can use regular URA drop out media.
Thanks Hanna. Yes I am using G418 in my plates and not kanamycin. I have tried using MSG but that did not work. I have heard adjusting the pH closer to 7 with NaOH can make G418 selection work while still using ammonium sulfate. I am trying it out tomorrow.
I guess you can try, however, the cell growth will be slower since the yeast medium should be acidic.
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