The quencher you select for your qPCR probes will ultimately depend upon the fluorophore chosen and the real-time qPCR machine you will be using. Most dark quenchers cover a relatively large range of wavelengths compared to traditional FRET components. They are typically divided into two general types: those that quench dyes in the green to yellow range and those that quench dyes in the orange to red range.
When working with dyes in the green to yellow range, ZEN™, Iowa Black® FQ, and Black Hole® Quencher-1 are all appropriate options. When working with dyes in the orange to red range, Iowa Black® RQ or Black Hole® Quencher-2 are appropriate. For dyes in the green to yellow range we highly recommend ZEN™ double-quenched probes as these products contain a second quencher located within the probe sequence itself. This additional quencher ensures that the dye’s fluorescent signal is quenched to a high degree for greater signal-to-noise ratios when compared to single-quenched probes.
You can configure your machine for dark quenchers by selecting black, dark, NFQ, or none as your quencher. This setting will vary from machine to machine but almost all qPCR machines are capable of utilizing dark quenchers.