MGB Probe Assays

Overview


Predesigned MGB Probe Assays are quantitative PCR assays for gene expression analysis. Each assay utilizes a Minor Groove Binder / Eclipse Dark Quencher (MGB:EDQ) probe, a proven high-performance chemistry that delivers exceptional target specificity, superior sensitivity, and remarkably low background signal. All three assay components—forward primer, reverse primer, and MGB:EDQ probe—are available in individual tubes or pre-mixed in a single clear tube, so you can move directly from gene target selection to confident quantification without time-consuming assay development. With a predesigned assay available for every gene, comprehensive transcriptome coverage has never been more accessible.


What Is an MGB:EDQ Probe?An MGB:EDQ probe is a single-stranded hydrolysis probe (used in the 5′ nuclease assay) bearing two key functional elements:

• A fluorescent reporter dye at the 5′ end
• A Minor Groove Binder / Eclipse Dark Quencher (MGB:EDQ) moiety at the 3′ end

In its intact state, the MGB:EDQ quencher inhibits the natural fluorescence of the reporter via fluorescence resonance energy transfer (FRET), keeping the background signal extremely low. During PCR amplification, the probe hybridizes to its specific target sequence and is cleaved by the 5′ exonuclease activity of DNA polymerase. This releases the reporter dye from the probe-target hybrid, generating a fluorescence increase that is directly proportional to the amount of target DNA present.


The MGB moiety (CDPI3, a tripeptide of dihydropyrroloindole-carboxylate) adopts a boomerang curvature that aligns with and binds strongly to the minor groove of B-form DNA. This groove-binding interaction provides significant additional stabilization of the probe-target duplex, enabling the use of shorter probes with optimized melting temperatures and enhanced specificity.

Predesigned MGB Probe Assays are currently verified for the following applications:

• Quantitative gene expression analysis (one-step and two-step RT-qPCR).

MGB:EDQ probe assays are highly prized inqPCR because they deliver performance advantages that standard Dual-LabeledProbes cannot match:

Feature:

• Minor Groove Binder moiety
• Shorter probes (typically 13 – 18 nt)
• Eclipse Dark Quencher (EDQ)
• Pre-mixed, single-tube format option
• Predesigned for every gene
• Compatible with all major qPCR platforms

Benefit:

• Dramatically stabilizes probe-target hybridization, enabling shorter probe designs with elevated Tm
• Enhanced discrimination of SNPs, splice variants, and closely related gene family sequences
• Non-fluorescent quencher produces negligible background, maximizing signal-to-noise ratio
• Eliminates multi-component setup steps; reduces pipetting error; saves time
• No assay development required; comprehensive whole-genome coverage
• No specialised instruments required; fits seamlessly into existing workflows

How to Order

1. Search by species and your gene of interest by gene name, gene symbol, or RefSeq accession number using the assay search tool above.
2. Select your assay and format from the results.
3. Add to cart.

For bulk orders, custom panel requirements, or assistance with gene target selection, please contact your local Merck representative.

6-FAM and HEX are trademarks of ThermoFisher Scientific.

FAM is a trademark of Applera Corporation or its subsidiaries in the US and/or certain other countries

HEX is a trademark of Applera Corporation or its subsidiaries in the US and/or certain other countries