The 1-base overhangs produced by AhdI may be hard to ligate. Sticky ends from different AhdI sites may not be compatible.
PciI is inhibited by nonionic detergents.
Sticky ends from different BspQI sites may not be compatible.
Sticky ends from different SapI sites may not be compatible.SapI gradually settles in solution, so a tube of SapI should be mixed before removing an aliquot.
Sticky ends from different BsmI sites may not be compatible.
FseI gradually loses activity when stored at -20°C.
Cleavage may be enhanced when more than one copy of the Bpu10I recognition sequence is present.
This recognition sequence is asymmetric, so ligating sticky ends generated by Bpu10I will not always regenerate a Bpu10I site.Sticky ends from different Bpu10I sites may not be compatible.
Prolonged incubation with NdeI may lead to removal of additional nucleotides.
Efficient cleavage requires at least two copies of the SfiI recognition sequence.
Sticky ends from different SfiI sites may not be compatible.
BsiWI is typically used at 55°C, but is 50% active at 37°C.
After cleavage, BamHI-HF® (but not the original BamHI) can remain bound to DNA and alter its electrophoretic mobility.
EcoRV is reportedly more prone than its isoschizomer Eco32I to delete a base after cleavage.