I have transformed my ligation product into DH5 alpha cells, after 1 day I got colonies which look transparent, round and inside the LB (amp). What can I conclude from that?
If you find a colony grows inside the media, it is possibly a contaminant. You should check your amp, it might have expired or no longer viable to use. Did you use Blue-White Screening?
Did you run a no ligase control plate? If you get lots of colonies from that, then your amp might be bad (or you have lots of the original vector present). If that clearish, inside the agar, colony is the only colony on the plate, then it can't hurt to grow it up and sequence it or do a diagnostic digest. If it's nothing, throw it out. If you have plenty of other colonies, then avoid that one weird one.
H there,
If you don't get any clone where you have actually plated your ligation mix and if clones don't look good it is not worth going further into analysis...
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