nonspecific primer extension products

Rafael Maldonado rafael at howard.genetics.utah.edu
Tue Feb 25 14:01:30 EST 1997


On 19 Feb 1997, Barr Lab wrote:

> After following the "RedBook" protocol for primer extension analysis, I
> observed bands that were both in the experimental and negative control
> lanes. These bands are intense (far too intense to be products from the
> transcript of interest), of specific sizes which are not dependent upon
> the sequence of the primer ( I get different sized bands for different
> primers). 

Could they be spontaneous stops of the polymerase? They are 
sequence-dependent, so they will appear in the same regions of the RNA 
even if you use several primers. You can use two primers separated by, 
say, 23 bp and see if the band appears in the same region.

Sometimes those stops are really annoying, indeed.

Rafa

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