HindIII

[C.S. Wilding]

I have some discrepancies between restriction digest results 
and sequence of PCR products. This concerns a HindIII site. 
In some of my samples a HindIII site is not predicted and 
this always matches with the digest, however in others a site 
is predicted but occasionally this does not cut. There can 
be, sometimes a partial digestion. It does not seem to be a 
heteroplasmy problem since the automated sequence output does 
not seem to be 2 peaks or even hint at this. I have tried 2 
batches of enzyme. I have tried PEG precipitation of PCR 
products to clean before cutting- this can help in inducing 
partial digestion when previously there was none.
My questions are- is HindIII prone to not cutting certain 
sequences for whatever reason? Is it perhaps "upset" by 
residual PCR reaction components? (I have tried getting rid 
of these with the PEG ppt). Has anyone any other ideas?
Cheers
Craig.