Several papers document that it is rather a myth than reality that an assay with hydrolysis probes (TaqMan®-assay) is superior to a SYBRGreen Assay  (Tajadini 2014, Cao 2012, Arikawa 2008). Provided that you design the right primer, use a high quality qPCR master mix like our primaQUANT and work with non-fragmented cDNA (same is true for TaqMan® assays as well).

Probe-based assays are especially suited for SNP-genotyping, for the analysis of splicing variants, and for the detection of mutations via qPCR.

If you are interested in gene expression or miRNA expression, SYBRGreen assays are to be preferred and allow additional quality parameters like melting curve analysis.

Our primaQUANT qPCR Mastermixes are available for SYBRGreen as well as for probes.

For more detailed information please see the following publications:

Tajadini, M., Panjehpour, M., & Javanmard, S. H. (2014). Comparison of SYBR Green and TaqMan® methods in quantitative real-time polymerase chain reaction analysis of four adenosine receptor subtypes. Advanced Biomedical Research, 3, 85.
Cao, H., & Shockey, J. M. (2012). Comparison of TaqMan® and SYBR Green qPCR Methods for Quantitative Gene Expression in Tung Tree Tissues. Journal of Agricultural and Food Chemistry, 60(50), 12296–12303.
Arikawa, E., Sun, Y., Wang, J., Zhou, Q., Ning, B., Dial, S. L., … Yang, J. (2008). Cross-platform comparison of SYBR Green real-time PCR with TaqMan® PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC) study. BMC Genomics, 9, 328.