I have tried several polymerase including fusion and KOD. Do you have recommendations concerning the annealing temperature and the PCR cycles?
I have had success using the Quikchange methodology (see Agilent web site), but only with Pfu turbo, not with Phusion. If it doesn't work (your plasmid is fairly big), make two overlapping PCR fragments bearing the desired fragments, fuse them by PCR using the distal primers and reclone them in your vector.
Good luck
I successfully used overlapping PCR to insert mutations in a sequence. You can make two fragments using standard PCR reactions and then fuse them using Overlap extension PCR. See the link http://link.springer.com/protocol/10.1007%2F978-1-60761-652-8_10
Hope this helps.
Rather than amplifying the entire 11 kb, you could use overlap PCR to create a smaller fragment (e.g., approximately 1-3 kb) that contains the mutation. Then use standard restriction digestion and subcloning to replace this fragment in your vector.
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