Can someone explain in some what simple terms why we can't use SYBR Green I master mix with Taqman probes?
Reason 1: SYBR green is a dye that starts to fluoresce once double-stranded DNA is generated from cDNA that it can intercalate into. Taqman may use different absorption spectra, you may look into details, e.g. FAM and TAMRA dyes.
Reason 2: Taqman AFAIK relies on break-up of a customized primer that is designed to fit a specific gene of interest. Simply adding another primer without SYBR dye won't help there. For details: http://en.wikipedia.org/wiki/TaqMan
In Taqman, there are three oligos, one for each end of the sequence to act as primers, and one that binds somewhere in the middle and is labeled with a fluorescent marker (probe). During the annealing phase all three oligos bind their target sequences. During amplification phase, the growing amplicon kicks off the fluorescently labeled oligo releasing it from a quencher and allowing it to fluoresce. That fluorescence is detected by the machine and counts as one copy of the sequence (or rather 2, since the opposite direction is not detected). Actually it's still mostly an estimation.
When you use SYBR Green there's no probe. Within the SYBR Green mastermix is a bunch of fluorescent dye that get incorporated into the growing amplicon. Copy number is estimated by the relative amount of fluorescence.
Pictures are better than words: http://www.intechopen.com/source/html/16794/media/image3.jpg
The meaning of detecting the fluorescence is different between the two forms. Perhaps someone else will know if there are differences in the polymerase or other things that actually prevent you using the mix with the Taqman. It's a waste to buy the expensive probes and not reap the benefit of the specificity they offer.
There is no reason why you cannot perform TaqMan assays in SYBR Green mastermix, provided you ensure that the dye used for the TaqMan probe can be differentiated from the SYBR Green. For example FAM and SYBR Green are incompatible because the have very similar emission wavelengths. TaqMan probes with TET, HEX or JOE reporters should work in SYBR Green mastermix.
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