I have been working with E. coli DH5 alpha competent cells to amplify my PLJM1 plasmid with an insert, but it just doesn't get amplified in the appropriate amount! The bacterial yield is too low as well. But the same plasmid with ERK-2-insert gets amplified in the same bacteria. The bacteria also seem to multiply plasmids very well in the lab next to ours. I have tried the amplification many times, and it's still just a very faint band in the gel. Totally clueless as to why this is happening when the same bacteria with the same plasmid but a different insert grows in the same media, but this doesn't.
You seem to write that the yield of bacteria is also low. This is likely the fundamental problem. Maybe the plasmid is toxic, or maybe that one specific culture is contaminated (for example by a phage).
Before getting too worried, I would take your plasmid DNA and do a new transformation and try again. If that still grow poorly then it may be the insert but I suspect it will fix the problem.
Thanks for the responses! I've actually solved the problem by switching over to NEB Stable 3 E. coli cells. Even that would'nt give a nice yeild in the beginning so I played around with the incubation conditions. Turns out when I allowed the bacteria to grow overnight at room temperature(had to leave the incubator door open), the plasmid's integrity was preserved and I got a very nice yeild.
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