ExoIII-Why not ApaI?

[Markus Piotrowski]

Hi netters,

somewhere I read, that some restriction enzymes -although leaving a 4 
base 3' protusion - can't be used to protect DNA in an ExoIII-digestion.
Fortunately I read this after using such an enzyme, ApaI, and I found 
that it worked well in my case.
The only problem was the complete removal of some bases (from the 
ApaI-site to the first base of the KpnI-site in pBs SK+) on the 
'protected' end.
Is this the reason why these enzymes shouldn't be used or why are they 
not recommended?

Greetings, Markus
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