Colored DNA after phenol extraction - Strange color in aqueous phase and degraded DNA... (Apr/15/2009 )

Hi everybody!

I'm working with acidophilic bacteria, trying to extract their genomic DNA by the phenol-chloroform method. For most of my bacteria this method works fine, but for one of them in particular the DNA always get degraded. And the most strange part is that the bacterial lysate is a bit reddish, and after the first addition of phenol, the aqueous phase turns REALLY red . The final DNA pellet also retains some of this color. And as I said, most of the DNA turns out to be degraded .

I have read that in plants there are lots of secondary metabolites that can interfere with DNA extraction and ultimately degrade it... Did anyone has this problem with DNA extraction in bacterias? How can I get rid of this "secondary metabolite"? Any detergent or substance that may help?

Any suggestions please!! thanks!

You could try the CTAB extraction in Sambrook, which is used for plant DNA extraction, where phenols are common contaminants.