The correct reporter dye will depend on the type of instrument you are using and the compatibility of the dye with the instrument. For multiplexing applications, we recommend using reporter dyes with the least amount of spectral overlap.
Use our Multiplex Dye Selection Tool to help choose appropriate dyes and quenchers for your instrument. In addition to planning multiplex qPCR experiments, you can also use this tool as a good reference to see which dyes are calibrated on your instrument, as well as which alternative dyes are compatible with your instrument after calibration. If needed, use the Add to Wish List button to save your multiplexing recommendations.
For a list of selected IDT dye and quencher combinations, please see the Dye and Quencher Compatibilty Table. For a list of reporter dyes compatible with common instrumentation, see the Instrument Compatibility Table.
Traditional dark quenchers absorb broadly and do not emit light, which allows for use of varying reporter dyes with a given quencher and for expanded options in multiplex assays. Dark quenchers simplify detection, which makes them compatible with a broad range of image analysis instruments.
IDT has developed two internal quenchers that enables the production of Double-Quenched Probes, which have less background and more signal.
- ZEN™ Double-Quenched Probes contain a 5’ FAM fluorophore, a 3’ IBFQ quencher, and an internal ZEN quencher
- TAO™ Double-Quenched Probes contain a Cy® 5 fluorophore, a 3’ IBRQ quencher, and an internal TAO quencher
These Double-Quenched Probes are an improvement over traditional dual-labeled probes and have consistently low background, reduced Cq values, improved precision, and enable the use of longer probes for design in AT-rich regions. For more information download the PrimeTime® Custom qPCR Probes Flyer.
IDT supplies other commonly used dark quenchers as well as the proprietary dark quenchers (Iowa Black® FQ, Iowa Black RQ) and the internal ZEN and TAO quenchers. TAMRA is also a quencher option for a FAM reporter dye.