Restriction digestion of PCR fragments

[B VISSER * x2818 Plantkunde *]

Hi

I am in the process of digesting amplified cDNA fragments with Not1 of which 
a restriction site was incoporated into the primers.  I am not able to fully 
digest the fragments, even though sufficient nucleotides are present on the 
5' side of the restriction site.  Could Ethidium bromide play a role in the 
inhibition of the digestion of the DNA?  I usually run the fragments on a 
prep gel and cut the desired fragments from the gel with phenol/chloroform 
which is followed by a ethanol precipitation.  Could this be the reason?

Botma Visser