title: Modified tetra-primer ARMS PCR as a single-nucleotide polymorphism genotyping tool.
abstract: OBJECTIVE
  Genotyping of single-nucleotide polymorphisms (SNPs) has been applied in various genetic contexts. Tetra-primer amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) is reported as a prominent assay for SNP genotyping. However, there were published data that may question the reliability of this method on some occasions, in addition to a laborious and time-consuming procedure of the optimization step. In the current study, a new SNP genotyping method named modified tetra-primer ARMS (MTPA) PCR was developed based on tetra-primer ARMS PCR.
  
  
  METHODS
  The modified method has two improvements in its instruction, including equalization of outer primer and inner primer strength by additional mismatch in outer primers, and consideration of equal annealing temperature of specific fragments more than melting temperature of primers. Advantageously, a new computer software was provided for designing primers based on novel concepts.
  
  
  RESULTS
  The usual tetra-primer ARMS PCR has a laborious process for optimization. In nonoptimal PCR programs, identification of the accurate genotype was found to be very difficult. However, in MTPA PCR, equalization of the amplicons and primer strength leads to increasing specificity and convenience of genotyping, which was validated by sequencing.
  
  
  CONCLUSIONS
  In the MTPA PCR technique, a new mismatch at -2 positions of outer primers and equal annealing temperature improve the genotyping procedure. Together, the introduced method could be suggested as a powerful tool for genotyping single-nucleotide mutations and polymorphisms.
authors: Division of Cell and Molecular Biology, Department of Biology, Faculty of Science, University of Isfahan , Isfahan, Iran .
authors: Hamzeh
authors: H
authors: Mesrian Tanha
authors: Marjan
authors: M
authors: Mojtabavi Naeini
authors: Soheila
authors: S
authors: Rahgozar
authors: Seyed Mohammad Mahdi
authors: SM
authors: Rasa
authors: Sadeq
authors: S
authors: Vallian
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000032:analysis / Q000235:genetics; D017931:DNA Primers; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
chemical_list: D017931:DNA Primers; D004247:DNA