What is the difference between Black Hole Quencher (BHQ) dye and TAMRA?

There are several differences between BHQ dye and TAMRA. A major difference between the two is that BHQ is a darker quencher that re-emits its energy as heat. On the other hand, TAMRA re-emits its energy in the form of fluorescence. Because of this, nonspecific background fluorescence of TAMRA may reduce sensitivity of a TaqMan assay. Another difference between the two is that the use of BHQ results in a 1.2-2.8 fold decrease of intra-assay variability as compared to using TAMRA. A third difference between TAMRA and BHQ dye is that TAMRA is an effective quencher for fluorophores with emission maxima less than 560 nm. In contrast, BHQ have broad absorption ranging 480-580 nm (BHQ-1), 559-670 nm (BHQ-2), and 620-730 nm (BHQ-3); this is useful for a wide range of reporter dyes in multiplexed assays.