Black DNA from earthworms

[Patrick Weix]

<sjames at miu.edu> 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,

Patrick
-- 
                                             weix at netcom.com