enzyme problem - (Oct/26/2013 )

why does sal1 (or similar enzymes) have a problem digesting pcr products.?

i mean is it applicable after the pcr product is cleaned??

if so, whats the logic behind it??

I don't think anyone has studied this. It's just an observation (and, like many such observations, may be more anecdotal than true). There clearly is a length of DNA surrounding a SalI cut site which will make it behave similarly to an enzyme site in the middle of a piece of DNA, but it may be longer than the typical 6 bp. Many enzymes have site preferences, sometimes rather extreme.

thanks again..