restriction enzyme flanking sequence preferance - (Feb/20/2010 )
when adding restriction sites to a primer is the flanking sequence at the 5 end of restriction sites important and how many bases are required? Actually I have heard that new england biolabs suggests best sequence for each enzyme but I couldnt find it.
Check these two NEB pages:
I usually add 8 bp, but 6 is probably more than enough.
you donot need a specific sequence but a number of bases on either side of the restriction sites. I use 6 extra bases, but for some enzymes you might need 8.
NEB has the number of bases required for each enzyme.