In article <54859.sjames at miu.edu>, <sjames at miu.edu> wrote:
>> 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.
>> Sam James 515-472-1146 fax:515-472-1167 sjames at miu.edu
I did some work with total RNA extraction from tobacco root samples that
(unfortunately) contained 50% soil. I had no problems with the integrity
of the RNA or with the yeild (all that gritty soil helped the grinding no
end!). BUT the RNA was BROWN - ranging from light to v.dark to black. I
had no problems with it apart from quantifying it using a spec. When I ran
the samples in formaldehyde gels, ALL the brown "gunk" stayed in the wells.
Gina posted regarding removing humics from DNA extracted from sediment.
The suggestion was to run samples out on a gel to separate the DNA from the
humics which "tend to run faster".
Between denaturing gels and standard gels there should be a useful