Oligo stability in water at -20 C

Chris Boyd chrisb at hgu.mrc.ac.uk
Fri Aug 14 07:45:06 EST 1998


Hiranya Roychowdhury (hroychow at NMSU.EDU) wrote:

: At 01:31 AM 8/11/98 GMT, Michael T. MacDonell wrote:
(snip)
: >...degradation is actually attributable to nucleases.  How are can you be
: >sure you are not seeing nuclease degradation and believing that it to
: >be autocatalysis?
(snip)

: Dear Mike,
:         While nuclease may not be totally discounted in any situation,
: autocatalysis of nucleic acid is a fact. The reason I'm sure about this is
: that I had performed a simple expt a couple of years back. I made up two...
(snip)
: Dr. Hiranya Sankar Roychowdhury

Before this thread gets entirely taken over by water sports (a good
trick to try on students is to ask them to make up some 55.55M water),
I'd like to comment on the responses to the original question I posed.
First of all, I cannot believe that nucleases are responsible for the
oligo degradation we see. Everyone here uses autoclaved Milli-Q water
or buffer for dissolving oligos, and most do this with one-use
aliquots. So any nucleases present would have to be in the dried-down
oligos as received from the supplier. Another argument against
nucleases being responsible is the absence of Mg -- it's my
understanding that DNAses need Mg to work, so where is it coming from
in this situation?  (All right, if there are bugs present, there is Mg,
but I don't buy the bug-contamination argument as a general cause of
degradation either.) 

Secondly, it is noteworthy that no-one seems to know of published data
on autohydrolysis of DNA and I agree that Hiranya should publish his
results.

The bottom line is that Mike thinks there is no problem with
water-dissolved oligos, and Hiranya thinks there is. So erring on the
side of caution, surely it is wiser to dissolve oligos in TE rather
than water? Are then any possible DISadvantages of dissolving oligos in
TE?

Best wishes,
-- 
Chris Boyd                      | from, but not \ MRC Human Genetics Unit,
Christopher.Boyd at hgu.mrc.ac.uk  | on behalf of  /  Western General Hospital,
http://www.hgu.mrc.ac.uk/Users/Christopher.Boyd \   Edinburgh, EH4 2XU, SCOTLAND



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