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Double-quenched probes increase signal to noise ratios by decreasing background fluorescence

ZEN™ and TAO™ Double-Quenched Probes

Review data demonstrating that ZEN Double-Quenched Probes in qPCR assays provide improved signal to noise ratios compared to single-quenched probes. ZEN and TAO Double-Quenched Probes also make it more feasible to use longer probes due to the lower background fluorescence.

Including a second, internal quencher in qPCR probes decreases the distance between 5’ dye and quencher which, in concert with the 3’ quencher, provides greater overall dye quenching, resulting in decreased background fluorescence and improved signal to noise ratio (Figure 1A). IDT offers ZEN and TAO internal quenchers for use in double quenched probes. 

The additional ZEN or TAO quencher also increases assay efficiency, as illustrated by a decreased number of cycles required to meet the signal threshold (Ct) compared to single-quenched probes (Figure 1B). This can be critical for identifying targets that are limited due to small sample size or low target expression. In fact, the use of ZEN Double‑Quenched Probes rather than standard single-quenched probes enabled applications that were not previously possible due to very high signal to noise ratio requirements when measuring low picomole quantities of dNTPs [1].

Improved qPCR results with ZEN Double-Quenched Probes 

Figure 2 shows that the decrease in background fluorescence obtained when using double-quenched probes is also evident with longer probes. The ability to use longer probes without sacrificing assay quality provides greater flexibility when designing experiments. For example, when interrogating regions of low complexity, it may be necessary to design longer probes to obtain a higher Tm. Unlike single-quenched probes, ZEN Double‑Quenched Probes exhibit low background fluorescence even when 40 nt long (Figure 2).

low background even with long probes with ZEN Double-Quenched probes 

Use of ZEN and TAO Double-Quenched Probes provides researchers with increased precision and design flexibility in their qPCR experiments. qPCR probes that include the ZEN or TAO quencher (Double-Quenched Probes) can be ordered online from our PrimeTime™ qPCR Probes page.


  1. Wilson P, Labonte M, Russel J,  et alA novel fluorescence-based assay for the rapid detection and quantification of cellular deoxyribonucleoside triphosphates. Nucleic Acids Res, 1(39):e112.

RUO—For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations. RUO22-1594_001

Published Sep 16, 2013
Revised/updated Feb 17, 2023

Black Hole Quencher™ is a trademark of Biosearch Technologies, Inc. Licensed from BTI for RUO.