I am planning to standardize a TaqMan duplex PCR assay for allelic discrimination. I intend to use FAM and TAMRA for one probe. Which dye and quencher would be best for the second probe that can work efficiently in combination with FAM?
This depend from the type of instrument of qPCR. In case is possible to use JOE or VIC (~550 nm), CY3 or (~ 580 nm, but is the same of TAMRA), TEXAS RED (~ 610 nm, but is the same of ROX), CY5 (~ 650 nm).
Giorgia Pertile Are JOE & VIC open chemistry like FAM or patented one. Can I use HEX or Yakima Yellow dye instead?
Yes is the same of FAM. When you order your probe, you need to label at 5' with JOE or VIC or FAM and at 3' with the quecer (this depend of which type of dye you use). You need to chose the dye in function of the spectra emission and in function of the dye is possible to detect from your qPCR.
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