Enhanced allele-specific PCR discrimination in SNP genotyping using 3' locked nucleic acid (LNA) primers

Hum Mutat. 2003 Jul;22(1):79-85. doi: 10.1002/humu.10228.


The specificity and reliability of locked nucleic acid (LNA) substitution at the 3' position of allele-specific PCR (AS-PCR) primers for SNP detection was investigated in direct comparison to DNA primers. Both plasmid and human genomic DNA templates were examined in this study. All possible DNA and 3' LNA mismatch combinations were tested in triplicate with the plasmid target. LNA primers yield consistently low amounts of mismatch products with all base combinations, whereas certain mismatches with DNA primers generate strong false positive amplicons. Amplified human SNP alleles within the cystic fibrosis (CFTR) gene were analyzed in AS-PCR by gel analysis and real-time fluorescence generation. A 3' LNA residue in the primer at the SNP site improves allelic discrimination and functions under a wide window of PCR conditions. We demonstrate increased AS-PCR specificity with comparable sensitivity using 3' LNA primers in gel electrophoresis and real-time detection experiments. This increase in AS-PCR discrimination with 3' LNA primers should facilitate the use of this simple, rapid, and inexpensive technique for SNP genotyping applications.

Publication types

  • Comparative Study

MeSH terms

  • Alleles*
  • Base Pair Mismatch / genetics
  • Computer Systems
  • Cystic Fibrosis Transmembrane Conductance Regulator / genetics
  • DNA Mutational Analysis / methods
  • DNA Probes / genetics
  • Genotype
  • Humans
  • Nucleic Acid Hybridization / genetics
  • Nucleic Acid Hybridization / methods
  • Oligonucleotide Probes / chemistry
  • Oligonucleotide Probes / genetics*
  • Plasmids / genetics
  • Polymerase Chain Reaction / methods*
  • Polymorphism, Single Nucleotide / genetics*
  • Sensitivity and Specificity


  • CFTR protein, human
  • DNA Probes
  • Oligonucleotide Probes
  • cystic fibrosis transmembrane conductance regulator delta F508
  • Cystic Fibrosis Transmembrane Conductance Regulator