cleaning PCR primers

Steve Hopkins shopkins at
Mon Dec 12 17:28:38 EST 1994

>We have just made some oligos for PCR on a 50pmol scale, cleaved them from 
>the column, deprotected and dried them down.  When they are redissolved in 
>water there is visible rubbish in the tube, which does spin down.  I have 
>tried using the clear supernatant, diluted, in a PCR reaction and get 
>nothing.  My question is, does anyone know if dirty primers can inhibit the 
>PCR reaction?  And if so what is the best method (and simplest) for 
>cleaning them up?>Jo Caine

We received some commercially prepared primers in a similar state, which did 
not work properly. The issue was not resolved entirely, but seemed to be 
due to material coming off the column. The material from the column 
resulted in a spuriously high OD value, resulting in over dilution of the 
primers (i.e. it was difficult to know how much primer we had), rather than 
the dirty primers interfering with PCR. 

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