Primer Degradation?

Pam Snyder snyder.9 at
Fri Oct 3 17:14:07 EST 1997

In article <gilbride-3009971316320001 at>, gilbride at
(Kevin Gilbride) wrote:

> I need some advise regarding the stabilty of primers. I am using a primer
> set which consists of a 25 and 22 mer oligos with a balanced AT / CG
> content. My main concern is a laddering of bands appearing in the dH2O
> control lanes. It is not a contamination, my other primers are free of
> this problem, including Beta Globin and Actin sets. My water source
> remains constant and when I have tried other sources the problem persists.
> I have tried storage at 4º, -20º and -80º avoiding multiple freeze thaw. 
> The primers were synthisized by Oligo's Etc. they work initially upon
> arrival but soon after the waters show these bands, it wouldn't be that
> bad but they are in right in the range of which my positive bands appear.
> Any advise or comiseration would be welcome.       
> Thanks
> KJ Gilbride
> Mallory Institute of Path.
> gilbride at

"clean" primers are stable.  Do you store master (concentrated) stocks
separate from your working stocks?  Then anytime you see  something odd
you go back to you masters and see where the problem is starting. 

 It also greatly limits the # of times primers master stocks are
frozen/thawed/pipeted.  We make multiple working stocks from the masters
in 1 ml vols, and further aliquots these to 200ul aliquots and use them
one at a time.  If we have any reason to suspect an aliquot, we pitch it. 
We have masters that have remained clean and intact for 8 years.  

Why do you think that contamination is not a problem?

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