Multiplex qPCR · SNP genotyping · diagnostic assay panels
Dual-Labeled Probes
Pre-validated reporter-quencher pairs for TaqMan qPCR probes, molecular beacons, and multiplexed detection — optimized for signal-to-noise and compatibility with standard instruments.
| Category | Sub-category | Name (full) | Code | Applies to | Position | Function & mechanism (EN — for website copy) | Typical applications |
| Dual-Labeled Probes | Standard qPCR combinations | FAM + BHQ1 | FAM-BHQ1 | DNA | 5′ FAM / 3′ BHQ1 | Most widely used TaqMan probe combination. FAM emission at 520 nm is efficiently quenched by 3′ BHQ1 (~480–580 nm absorption). Excellent signal-to-noise ratio for standard qPCR. | Standard TaqMan qPCR, gene expression, viral load quantification |
| Dual-Labeled Probes | Standard qPCR combinations | FAM + BHQ2 | FAM-BHQ2 | DNA | 5′ FAM / 3′ BHQ2 | Alternative FAM combination using BHQ2 as quencher. BHQ2 has broader absorption compared to BHQ1; preferred when high quenching efficiency is needed for longer probes. | Long TaqMan probes, alternative quenching strategy |
| Dual-Labeled Probes | Standard qPCR combinations | FAM + MGB | FAM-MGB | DNA | 5′ FAM / 3′ MGB | Gold standard for SNP genotyping. MGB raises Tm sufficiently to enable 13–20 nt short probes with single-base specificity. BHQ1 quenching typically added near FAM. | TaqMan SNP allelic discrimination, allele-specific qPCR |
| Dual-Labeled Probes | Standard qPCR combinations | HEX + BHQ1 | HEX-BHQ1 | DNA | 5′ HEX / 3′ BHQ1 | Second-channel probe for multiplexed qPCR alongside FAM. Enables simultaneous two-target detection in the same reaction. | Duplex qPCR (with FAM), internal control detection |
| Dual-Labeled Probes | Standard qPCR combinations | CY5 + BHQ2 | CY5-BHQ2 | DNA | 5′ CY5 / 3′ BHQ2 | Far-red probe combination for four-plex qPCR. Minimal spectral overlap with green-channel probes. Requires far-red detection capability. | 4-plex qPCR, respiratory panel diagnostics, multiplexed SNP typing |
| Dual-Labeled Probes | Standard qPCR combinations | CY5 + BHQ3 | CY5-BHQ3 | DNA | 5′ CY5 / 3′ BHQ3 | Optimized far-red probe using BHQ3 matched to CY5 absorption peak. Provides superior quenching for CY5 vs BHQ2. | Far-red multiplex qPCR, high-performance CY5 probes |
| Dual-Labeled Probes | Standard qPCR combinations | ROX + BHQ2 | ROX-BHQ2 | DNA | 5′ ROX / 3′ BHQ2 | Third-channel probe for three-plex qPCR. ROX is also used as a passive reference dye in some instruments. | Triplex qPCR (with FAM and HEX), multi-pathogen panels |
| Dual-Labeled Probes | Standard qPCR combinations | VIC + BHQ1 | VIC-BHQ1 | DNA | 5′ VIC / 3′ BHQ1 | Standard SNP genotyping probe combination for Applied Biosystems instruments. VIC is the second allele reporter in TaqMan SNP assays. | TaqMan SNP genotyping, Applied Biosystems platforms |
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