Eurogentec offers a wide range of fluorophores and quenchers in various combinations to fit any methods and Real-Time Thermocyclers. If any help is needed concerning the combination of dyes that should be used on a specific thermocycler, please do not hesitate to contact our scientific support that will be happy to help you.

Dye combinations

Although Eurogentec has the possibility to offer many different combinations of fluorophores and quenchers for dual labelled oligonucleotides, we recommend the combinations as mentioned in Table 1. For singleplex Real-Time qPCR we recommend FAM-BHQ1™ or FAM-Eclipse™ Dark Quencher Double Dye probes. FAM-TAMRA Double-Dye Oligonucleotides can also be used as a cost effective alternative. For multiplex Real-Time qPCR we recommend to use non fluorescent quenchers such as Black Hole Quenchers™, EclipseTM Dark Quencher or Deep Dark Quenchers. The use of dark quenchers reduces the background and therefore increases the sensitivity of the assay. 

For multiplex Real-Time qPCR, it is also very important to select dyes with a good spectral separation to avoid overlap of the signal. In general Yakima Yellow® is a good second dye, which can be detected by almost any Real-Time thermocycler. The third and fourth dyes are mainly depending on the filter settings of the cycler.