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Table 2 Mismatch discrimination for various primer designs at the SMAD7 rs4939827 SNP locus

From: RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers

3'-Primer Sequences Cq values
  (T/T) (C/C) ΔCq
...AA 26.0 26.0 0.0
...AAC 28.0 26.0 2.0
...AAT 25.8 26.7 0.9
...AACA 28.2 26.1 2.1
...AATA 25.6 26.1 0.5
...AAC aGGAC-x 27.9 26.7 1.3
...AAT aGGAC-x 26.9 26.4 0.5
...AAcAGGA-x 38.7 26.6 12.1
...AAuAGGA-x 27.9 40.5 12.6
...Aa CAGG-x 36.4 27.5 8.8
...Aa TAGG-x 26.2 28.8 2.6
  1. Amplification reactions were performed in real-time mode using SYBR® Green detection and either homozygous C/C or homozygous T/T human genomic DNA. Reactions were run in triplicate; average Cq values are shown. ΔCq represents the difference between the Cq value for the mismatched reaction minus the Cq value for the matched reaction. Sequences at the 3'-end of the primers are shown. DNA bases are uppercase and RNA bases are bold lowercase. The C3 spacer blocking group is indicated by "x". The location of the mismatch in the primer compared to the target nucleic acid is underlined.