PCR and qPCR
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Improve the specificity of SNP genotyping

Limit primer dimers and off-target artifacts with rhAmp™ SNP genotyping

Single-nucleotide polymorphisms (SNPs) and their associated phenotypes provide crucial information for elucidating gene function, identifying species or individuals, diagnosing diseases caused by gene variation, and selecting targeted therapies. PCR-based genotyping is a fundamental technology in molecular biology and genetics, as it allows labs to quickly and inexpensively determine genotype using high-throughput processing and low sample input.

However, as with all methods, there are limitations to consider. A significant concern for PCR genotyping assays is that the primers and probes can bind to incorrect targets and form primer dimers. At best, these non-specific interactions affect signal levels and create challenges for analyzing your data; however, they can make the data unusable.

In the recorded webinar, rhAmp SNP Genotyping: A novel approach for improving PCR-based SNP genotyping, Dr Scott Rose presents the groundbreaking technology used in rhAmp SNP genotyping assays that greatly reduces primer dimers and off-target artifacts. The method relies on activation of novel RNA-DNA hybrid primers by an RNase H2 enzyme, only when the primers are hybridized to their specific target. Importantly, the RNase H2 enzyme functions optimally under conditions that are compatible with Taq polymerase activity and cycling, such that there are no additional steps beyond those required for a normal PCR genotyping reaction. Watch the recorded webinar below to find out how the technology works, and how it can improve your genotyping experiments.


Product focus—tools for genotyping

rhAmp™ SNP Genotyping System

Improve the precision of your PCR-based SNP genotyping with rhAmp SNP Genotyping technology. This technology uses a unique two-enzyme system coupled with RNA-DNA hybrid primers to precisely interrogate target SNPs. Combined with IDT universal reporter chemistry, the rhAmp SNP Genotyping System offers a simple, high performance genotyping solution at an affordable price.

  • Generate the highest level of performance with greater than 99.5% call accuracy for over 90% of assays tested.
  • Interrogate SNPs in difficult sequence regions with amplicons sizes as small as 40 bp.
  • Validate markers affordably using the smallest pack size commercially available.
  • Ensure confidence in your data with gBlocks® Gene Fragments as control templates.

The rhAmp SNP portfolio includes all components needed to successfully generate high quality genotyping data on any commonly available real-time PCR instrument.

Learn more about the rhAmp SNP Genotyping System »


LNA PrimeTime® Probes

LNA PrimeTime Probes are dual-labeled DNA probes designed for use in 5′ nuclease assays. LNA-modified bases enable use of shorter probes with higher melting temperatures compared to probes with unmodified DNA bases. They are commonly used for custom applications such as transcript variant detection or research in microbial species.

Learn more about LNA PrimeTime Probes »


MGB Eclipse® Probes

MGB Eclipse Probes and companion primers are available for use in human, in vitro diagnostic applications. These are 5′ nuclease assays that incorporate probes containing a minor groove binder. These primers and probes are produced using our ISO 13485 certified production process for use as components in clinical diagnostic tests.

Learn more about MGB Eclipse Probes »

Additional reading

rhPCR SNP genotyping method provides confidence calls with >99.5% accuracy—Use this simple, single-tube genotyping platform to get >99.5% call accuracy. The method is based on RNase H2–dependent PCR technology and uses RNA-DNA hybrid primers, blocked at the 3′ end, that prevent primer-dimer artifacts and non-specific amplification.

Review other DECODED Online newsletter articles on PCR and qPCR applications.

You can also browse our DECODED Online newsletter for additional application reviews, lab tips, and citation summaries to facilitate your research.


Author: Hans Packer, PhD, is a scientific writer at IDT.


© 2017 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see www.idtdna.com/trademarks.


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