What is the difference between Black Hole Quencher (BHQ) dye and TAMRA?
TAMRA dye is an effective quencher for fluorophores with emission maxima less than 560 nm. Dyes with longer wavelength emissions will not be effectively quenched by TAMRA. In addition, TAMRA has its own fluorescence which complicates data analysis due to crosstalk between the channels. In contrast, Black Hole Quencher™ dyes are true "dark" quenchers with no fluorescent signal. Their use simplifies design, implementation and interpretation of qPCR assays.
Furthermore, BHQ™ dyes have broad absorption spanning 480-580 nm (BHQ-1), 559-670 nm (BHQ-2) and 620-730 nm (BHQ-3), to enable use of a large range of spectrally distinct reporter dyes in multiplexed assay designs. With some dye pairings, FRET quenching is supplemented by the static quenching mechanism. Specifically, hydrophobic and electrostatic interactions facilitate the association of BHQ dyes with certain reporters to form an intramolecular dimer, for enhanced quenching and improved signal to noise ratios. Thus, BHQ dyes may quench some fluorophores whose emission spectrum is beyond the limits of BHQ absorption. For more information on FRET and static quenching mechanisms in qPCR please visit our Quenching Mechanisms in Probes website.