My lab is planning to work on multiplex qPCR to detect multiple organisms from clinical sample. We are now ordering the primers and probes.
However, I found single quenched probe and double-quenched probe, not really sure which one better is for multiplexing, or even is there any difference at all?
Can anyone help me out here for this?
Double quenched probes are certainly better! they increase the sensitivity by reducing the background flouroscence so target genes at a very low levels can also be detected. But then you need to optimize your run cycles for double quenched probes.
We are also going to develop a multiplex real-time PCR assay (4-plex) with double quenched probes. Do you think the thermal protocol should be specifically optimized for double quenched probes? Thank you
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