3 way ligation help needed - (Nov/13/2009 )
According to NEB:
Q14: Is there a difference in cutting close to the ends between NotI-HF and NotI?
A14: No. When tested on a series of five oligos (19-23 bases in length) containing the restriction site and an additional 1 to 5 A/T bases from the end, both enzymes cut the oligo with 1 base pair from the end. When designing primers, NEB recommends adding 6 extra bases to ensure against experimental failure due to variation in substrate and reaction conditions.
So the NotI should cut and the XhoI I have is an aliquot from another lab which claims they use that same tube regularly with no difficulties.