I have problems with plasmids, retransforming them or use them in mammalian cell culture. I recently discovered only the samples I transfected with plasmids have contamination sometimes red, sometimes colorless but stinky, or some bigger organism not bacteria. Could it be that my DNA is contaminated? If so how can I save it? I have several constructs I don't want to clone each of them again.
If you think your plasmids are contaminated there are two things you could try. First you could just treat the tubes of plasmid at high temperature to kill bacterial of fungal contamination. I would suggest 15 minutes at 80oC would suffice for most microbes and won't impact your DNA.
The better approach would be to just transform a tiny bit of your plasmid DNA into fresh competent cells and select on appropriate drug plates. Then do another plasmid prep and those should hopefully be sterile. It may be that you introduced some contaminants with dirty pipet tip for example.
Plasmid DNA from a DNA extraction kit won't have any cells in it. You can even dry down plasmids by putting them on sterile filter paper and letting the liquid evaporate.
I'd also vote to set up a new plasmid prep, you should be able to get the frozen transformed cells out of the freezer. Or set it up yourself to be really sure that it's the plasmid you want.
You could have accidentally contaminated the tube with your plasmid, but given that you're seeing a bunch of different cell types it means that one or more of your tools or reagents are contaminated. Have a lab member who doesn't have contamination issues teach you more about sterile technique. It's really easy to accidentally "break the sterile field" with cultured cells. You'll get better with practice, good luck!
In my experience, contamination originating from the plasmid DNA used for transfection is relatively uncommon. It's more likely that other reagents, like the transfection buffer, are the source of the issue. Nevertheless, the simplest way to ensure your plasmid isn't the problem is to prepare a fresh batch via a new maxiprep (requiring re-transformation if you lack a glycerol stock).
I agree with Daniel Martin that contamination of the plasmid DNA is unusual. Still, one quick and simple way to kill most microorganisms would be to ethanol precipitate the DNA. Michael J. Benedik's suggestion to heat the DNA would also work.
You can always filter out any organisms by appropriately sized filters (just watch out for pDNA sticking to some materials). Only some viruses could be a problem.
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