Removal of PCR inhibitors

Dr. Duncan Clark Duncan at
Wed Nov 24 10:47:07 EST 1999

In article <383bddbc.49782822 at>,
jkcarson at writes
>If we use a 9ul volume of  template DNA prepared using the guanidinium
>method we do not get any PCR product but if we use a 1ul volume as
>template the PCR works. We have concluded that an inhibitor is
>co-extracting. BSA does not neutralise the effect.

SDS lysis of cells? I presume you do an ethanol or methanol based wash
of the diatoms to get rid of the guanidine prior to eluting with water
or TE? Are you acid washing the diatoms prior to use or autoclaving them
or what?

What will mess up the PCR is SDS, ethanol/methanol or guanidine traces
left behind and eluting with the water.

If using SDS try substituting Triton X-100 as per recent Indian lab's
Analytical Biochem paper - the author has posted in this newsgroup
recently so check the archives.

Do extra washes. 

Dry the diatoms better to drive off the ethanol/methanol.

Primarily elute with water - not TE. Reason 9ul of TE with 1mM EDTA in a
20ul PCR will chelate out 0.675mM Mg of your 1.5mM Mg. Adding in extra
Mg would compensate or maybe eluting with TE (0.1mM EDTA). Alternatively
use EDTA.

Let us all know what the answer is.


The problem with being on the cutting edge is that you occasionally get 
sliced from time to time....

Duncan Clark
DNAmp Ltd.
Tel: +44(0)1252376288
FAX: +44(0)8701640382

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