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PCR Allele Competitive Extension (PACE™) genotyping

  1. PCR Allele Competitive Extension Genotyping

Overview

IDT has partnered with 3CR Bioscience (UK) to provide a PCR-based SNP and indel genotyping system—PACE, or PCR Allele Competitive Extension, genotyping. Free primer design is provided. The primers are subsequently synthesized by IDT, a leader in oligonucleotide synthesis. 3CR Bioscience provides the PACE Genotyping Master Mix. Together these reagents yield cost-effective, specially designed genotyping assays that allow increased throughput without compromising data quality.

Partnering to provide high-quality, high-throughput genotyping

IDT has partnered with 3CR Bioscience (UK) to provide a PCR-based, SNP and indel genotyping system—PACE, or PCR Allele Competitive Extension, genotyping. Free primer design is provided. The primers are subsequently synthesized by IDT, a leader in oligonucleotide synthesis. 3CR Bioscience provides their high-performing PACE Genotyping Master Mix. Together these reagents yield cost-effective, specially designed genotyping assays that allow increased throughput without compromising data quality.

What is PACE genotyping?

PACE™ (PCR Allele Competitive Extension) genotyping is a fluorescent, competitive allele-specific PCR genotyping technology. It is ideal for biallelic discrimination of single nucleotide polymorphisms (SNPs) and insertions and deletions (indels) at specific loci.

Who should use it?

The PACE genotyping system has been developed for genotyping at any scale. Thus, this methodology can be of particular benefit to researchers performing high-volume experiments with large sample sets, such as in plant breeding projects.

How does PACE genotyping work?

PACE genotyping chemistry has 2 parts:

  1. Assay mix—comprised of 2 allele-specific forward primers and one common reverse primer
  2. Master mix—containing all of the components required for the PCR assay and generation of fluorescent signal

Each forward primer contains a tail sequence that corresponds with 1 of 2 universal FRET (fluorescence resonant energy transfer) cassettes in the master mix: one labelled with FAM dye and the other with HEX dye. During thermal cycling, the relevant allele-specific primer binds to the template and elongates, thus attaching its tail sequence to the newly synthesized strand. The complement of the allele-specific tail sequence is then generated during subsequent rounds of PCR, enabling the FRET cassette to bind to the DNA. Once bound, the dye within the FRET cassette is no longer quenched and emits fluorescence.

If the genotype at a given SNP is homozygous, only 1 of the 2 possible fluorescent signals will be generated. If the genotype is heterozygous, both fluorescent signals will be generated.

PACE Genotyping Master Mix is offered without ROX normalizing dye, or with high ROX (500 nM), standard ROX (150 nM), or low ROX (25 nM). When working with crude samples that contain large amounts of PCR inhibitors, the PACE-IR™ Genotyping Master Mix, which counteracts these inhibitors, is also available with and without ROX dye.

Get started with genotyping based on PACE technology

Get started with IDT and 3CR products for PACE genotyping.

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