DNA turns black over time - contamination?

[AngelaT]

Hi all! Thanks in advance for your help.

In our lab we have been noticing something strange. Over time, some of our DNA samples turn a black color. It does seem to settle at the bottom of the tube, like it's some sort of precipitate or soild. We are concerned that it might be fungal growth of some kind.

The samples are stored at -20C. We usually extract from Qiagen or Nucleospin kits, so they would be eluted in their respective buffers. We have not seen this black stuff in any of our reagents.

Has anyone seen anything like this before?

[Cooks]

Hi, these are probably isolation beads from the Qiagen kits. You can check if they are magnetic by placing them on a magnetic rack. We get DNA from an automated isolation pipeline all the time with these beads inside. We usually just remove them with a desktop centrifuge or magnetic rack.

[AngelaT]

Thanks for your reply! I did find out for sure that these kits do not use magnetic beads, so it's not that.

We've pretty much just assumed it was some kind of bacterial or fungal growth, especially because it's gotten worse over time. I was just hoping to find someone else who has experienced this and maybe learn more about what it is.

[fchatonnet]

Hi AngelaT, this looks indeed like a fungal contamination.
What buffer do you use to elute your DNA? Water, Tris EDTA ?
It might be worth either to filter your eluted DNA with a 0.22 µM syringe filter (be careful with the pressure, and also you will loose a bit of your samples due to the dead volume of the syringe and filter).
You may also add 0.01% sodium azide to your sample as an anti-contamination agent, but be careful this is a very nasty chemical so use it with adapted protection equipment (lab coat, gloves, goggles...)
Hope that helps and good luck!