How are the mismatch primers designed?
Back to the FAQ When a natural restriction enzyme site can not be found to genotype the SNP, one single-base mismatch will be introduced close to 3′ end of one primer that is near the SNP site to create an artificial restriction site. This allows restriction recognition sequences to cover the mismatch base and SNP site. This artificial enzyme recognition site is introduced in just one of the two allelic sequences. With the mismatched left or right primer as input, the Primer 3 program is used to design another paired primer.
