What Black Hole Quencher® do you recommend for dyes with long wavelength emissions, such as the Quasar® and Pulsar® dyes?
The BHQ®-2 dye is our preferred quencher for long wavelength fluorophores. This recommendation relates to the ease of manufacture using BHQ-2 over BHQ-3 dye. While both dyes represent excellent quenchers, the final yield is usually higher with BHQ-2 modified oligonucleotides, thus providing a more cost-effective synthesis with excellent purity and performance characteristics.
In the context of Dual-labeled BHQ probes, the BHQ-2 dye is an excellent quencher for long wavelength emitters such as Quasar® 670, Quasar 705, and Pulsar® 650. 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. More information on FRET and static quenching can be found on our Quenching Mechanisms in Probes webpage.