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.
| Dual-Labeled Probes | ||
| FAM-BHQ1 | FAM-BHQ2 | FAM-MGB |
| HEX-BHQ1 | CY5-BHQ2 | CY5-BHQ3 |
| ROX-BHQ2 | VIC-BHQ1 | |
FAM + 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.
FAM-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.
FAM + 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.
HEX + BHQ1:Second-channel probe for multiplexed qPCR alongside FAM. Enables simultaneous two-target detection in the same reaction.
CY5 + BHQ2:Far-red probe combination for four-plex qPCR. Minimal spectral overlap with green-channel probes. Requires far-red detection capability.
CY5 + BHQ3:Optimized far-red probe using BHQ3 matched to CY5 absorption peak. Provides superior quenching for CY5 vs BHQ2.
ROX + BHQ2:Third-channel probe for three-plex qPCR. ROX is also used as a passive reference dye in some instruments.
VIC + BHQ1:Standard SNP genotyping probe combination for Applied Biosystems instruments. VIC is the second allele reporter in TaqMan SNP assays.
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