Primer1: Primer Design Web Service for Tetra-Primer ARMS-PCR

Abstract

Tetra-primer ARMS-PCR is used extensively as a low cost, single PCR assay requiring no post-PCR manipulation. The design of successful primers depends on a number of variables such as melting temperatures, GC content, complementarity and selection of mismatch bases. The optimal selection of primers can be achieved in an automated way using a program which evaluates candidate primers for a given sequence. The Primer1 software was developed originally for use in the context of restriction fragment length polymorphism analysis using gel electrophoresis. However, recent applications have been more diverse, reviewed here, and we present an overview of the Primer1 software for primer design and web-service. We have updated the Primer1 program, and provide more complete details of the implementation. We also provide test data and output. The program is now available on a new, efficient, LAMP web service for users at: http://primer1.soton.ac.uk/primer1.html

Glutamate receptor, metabotropic 7 (GRM7) gene variations and susceptibility to autism: A case–control study

“…Genotyping of the rs6782011 and rs779867 SNPs of GRM7 gene was done using of Tetra‐Primer ARMS‐PCR technique. Four primers for each SNP (Table ) were designed by means of the Primer1 software [Andrew Collins, ]. PCR was performed using Ampliqon Taq 2x red master mix.…”

Peer Review #2 of "Obesity in the Balinese is associated with FTO rs9939609 and rs1421085 single nucleotide polymorphisms (v0.1)"

“…The FTO rs9939609 and rs1421085 variants were detected using amplification-refractory mutation system (ARMS) polymerase chain reaction (PCR). Detection of rs9939609 was performed using a previously published primer sets (Fawwad et al, 2015) while detection of rs1421085 was done using a novel primer sets, designed using Primer1 (Collins & Ke, 2012) and BioEdit® Sequence Alignment Editor (Ibis Bioscience, Carlsbed, CA, USA). Lists of outer and inner primers for ARMS-PCR is described in Supplementary Table S1.…”

Evaluation of novel SNPs and haplotypes within the <i>ATBF1</i> gene and their effects on economically important production traits in cattle

“…According to the sequencing results, PCR restriction fragment length polymorphism (PCR-RFLP), forced PCR-RFLP and tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) methods were used to detect genotypes of Qinchuan and Jinnan individuals ( Table 2). The primers of PCR-RFLP and forced PCR-RFLP were designed by the Primer Premier 5 software, and T-ARMS-PCR primers were designed on the Primer1 website (http://primer1.soton.ac.uk/ primer1.html) (Collins, 2012;Ye et al, 2001). The genotyping methods used on different SNP loci were introduced as below: SNPs genotyped with the PCR-RFLP and forced PCR-RFLP methods: SNP3 and SNP5 were detected using the PCR-RFLP method, and the PCR amplification products were digested with DdeI and HhaI restriction enzymes.…”