I would like to set up a taqman multiplex qPCR assay. Instead of using different dyes in my probes, I think a quencher can be used for 2 reporter dyes, e.g. FAM -TAMRA and JOE-TAMRA.
It is possible, of course, but I recommend you to use other quencher such as BBQ or BHQ. TAMRA, as a quencher, is the worst option.
Regarding the fluorophore maybe other options (FAM and VIC, o FAM and Cy5) could be possible as well.
Good luck!
Thanks Hector for the answer. However, the filter in 7500/7500 fast system is not compatible with some of the quenchers (BBQ or BHQ). In addition, which platform do you use for probe synthesis, also recommend the quencher for Cy5
You can use BHQ quenchers in ABI 7500 systems. It is not required to select the quencher - you can select the option "none". It works. As Hector mentioned BHQ series quenchers are much better than TAMRA. Also check for spectral overlap between the excitation/emission of fluorophores, when you are multiplexing.
In every case you must look for emission spectra as far away from each other in nm scale. We use Cy5-BHQ3 next to VIC and FAM. Altough all options of the (CFX) software to compensate for spectral overlap are applied we se a lot of Cy5 fluorescence in the VIC channel. So I agree with the others to use BHQ-quenchers. We buy our probe at Eurofins and they can synthetise probes with BHQ quenchers.
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