So my vector PCR product will theoretically have an additional base at the end, where I designed overlapping primers for my insert. So the exonucleases in the InFusion master mix will chew back the ends of my vector and insert PCR products 5'>3'; however, I'll have an extra base on the vector site. Will this still work? I'm hoping the 3'>5' exonuclease activity of my DNA polymerase (Phusion) from PCR will generate some products that are missing this additional base.
Edited by Ahrenhase, 06 March 2014 - 12:34 PM.