Black DNA from earthworms

Patrick Weix weix at
Wed Jun 22 11:51:17 EST 1994

<sjames at> writes:

>I would like to know if anyone has encountered a similar phenomenon with 
>other critters.  When we do any of several standard DNA preps, we get a 
>very dark brown to black pellet that turns out to be DNA- it looks like 
>DNA to UV, it does ok when we try to amplify various genes, etc.  Why the 
>concern if it works?  It doesn't always work. Some worms yield darker DNA 
>than others, and there have been problems getting PCR reactions to go.  
>Magnesium manipulation sometimes helps, sometimes not.
>   It would be nice to know 1) what is this dark stuff, 2) how to get rid 
>of it, or 3) how to consistently work around it.  Yes, we have taken the 
>dirt out of the worms first.  Thanks to all, and I hope this is not a FAQ.

I doubt that this is a FAQ. I have encountered the co-purification of
pigments with DNA in two different systems: yeast ADE mutants and
melanocytes. Yeast ade1 and ade2 (I hope I am remembering this
correctly) produce a red pigment.  The older the cell colonies are,
the darker the pigment (likely just more of it).  
   Also, in purifying DNA from melanoma cell lines, the pigment will
co-purify with the DNA, giving me brown DNA preps.  So far, it has not
been a problem with PCR, but I only use 60ng of this mouse melanoma
DNA for a 20microl rxn. Perhaps you add too much DNA (more than is
necessary) and thus get too much pigment in the rxn?  I do not know
how you purify your DNA. Perhaps you could get it away from the
pigment with Elutips or one of the glass powder systems?

Good luck,

                                             weix at

More information about the Methods mailing list