SNP Genotyping with Real-Time PCR (qPCR) Assays

SNP Genotyping qPCR assays discriminate between single nucleotide variations within a target sequence. SNP detection assays have broad applications across many industries from agricultural biotechnology to pharmaceutical research. Dual-labeled, probe-based SNP genotyping takes advantage of the 5’-nuclease activity of polymerase in combination with two-channel fluorescence detection. One SNP assay contains two allele-specific probes that have a single base mismatch and a primer pair flanking the SNP target. Each allele-specific probe is labeled with its own fluorescent reporter dye and is paired with a quenching non-fluorescent BHQ® dye. The two probes will competitively bind the target sequence with only the matching probe recognizing the correct allele to release the fluorophore signal.

Choose BHQplus® Probes for Genotyping

  • Small but powerful: duplex stabilizers permit the design of shorter dual-labeled probes
  • High fidelity: shorter sequences offer an increased barrier against hybridizing to a mismatch
  • Proven performance: the Black Hole Quencher dye extinguishes fluorescence until target hybridization
  • A mouse-click away: design your BHQplus probe through LGC Biosearch Technologies’ free, web-based RealTimeDesign™ software
  • Bottom line: An economical alternative for probe-based SNP Genotyping

The modified base chemistry of these probes allows for compact designs providing excellent sequence discrimination of SNPs or difficult AT-rich target sequences.

BHQplus SNP genotyping probes provide resolution of genotypes across a wide dynamic range of starting target molecules.

Learn more by visiting our Genotyping - qPCR Applications page

Endpoint Genotyping Across
Serial Dilution of Template

SNP Genotyping Graph

RealTimeDesign Software Logo

You can easily design probes and primers for gene expression and SNP genotyping using our free, online qPCR assay design program called RealTimeDesign software.

If you already know your sequences* you can enter them into our online BHQplus order form.

*BHQplus probes utilize a separate and unique chemistry from MGB probes. MGB probe designs will not necessarily operate as BHQplus probes and may require some minor sequence modification. To check the design, please use our RealTimeDesign Software or contact for assistance.

ValuMix™ qPCR Assays for SNP Genotyping

Two custom BHQplus probes and a primer pair are delivered in exact quantities in one tube. This is a user-friendly delivery format that simplifies your qPCR setup by reducing pipetting steps for rapid, reaction setup times. Check out our ValuMix qPCR Assays product page for more details.

SNP Genotyping Dye Options
Probe Fluorophore Excitation Emission Quencher
Probe 1 (Fixed) FAM 495 nm 520 nm BHQ-1
Probe 2 (Select One) TET 521 nm 536 nm BHQ-1
CAL Fluor® Gold 540 522 nm 544 nm BHQ-1
CAL Fluor Orange 560 538 nm 559 nm BHQ-1

Genotyping with BHQplus® Probes Poster

See how BHQplus Probes perform. Download this scientific poster.