I have a pLEX 307 plasmid that has 3 BsmBI sites that I am trying to remove. 1 site is in the SV40 promoter, another site is in the PuroR sequence, and the last in the CmR sequence. I was able to design primers for point mutations in the SV40 promoter and CmR sequence with no problems using NEBs base changer tool.

The problem im having is with the BsmBI site in the PuroR. Its has 73% GC so when I use the NEB tool it gives me primers with a Tm of 80 degrees C. Same thing if I try a gibson assembly with a different PuroR sequence from another plasmid, it gives primers with a Tm of 75> . Not sure how to design primers so it works or if there's another method for removing the BsmBi site.