Subcloning dirty PCR products

[schupp at nauvax.ucc.nau.edu]

Sounds like incomplete digestion.  A few thoughts, sorry if you've already
had them.

        -purify the PCR product prior to restriction.
        -some enzymes are more sensitive to cutting at the end of a sequence
         than others.  New England Biolabs has some data on this in their
         catalog.
        -depending on the size of the fragment, you might be able to
         run the digested fragment on Synergel:agarose gel or a Metaphor
         gel against the uncut fragment to check the digestion.

Jim Schupp