Why is BHQ-3 not an option when selecting Quasar or Pulsar dye labels?
Although we do offer BHQ-3 as a modification for oligos, we do not offer it paired to Pulsar 650, Quasar 670 or Quasar 705. For those dyes, we recommend BHQ-2. We do have data showing that BHQ-2 would be the optimal quencher to use. If you look on the Biosearch website under the Dual-labeled Probes, you will see that we automatically paired Pulsar 650, Quasar 670 or Quasar 705 with BHQ-2: http://www.biosearchtech.com/store/product.aspx?catid=224,171,40 We generally do not recommend using BHQ-3 for Dual-labeled Probes since we cannot guarantee its results (minimum yield, functional performance, etc). It may be somewhat misleading when you look at the spectra of BHQ-3 compared to Quasar 670 because it is illustrating the traditional model of quenching and spectral overlap. It is possible that the principle quenching mechanism is not FRET but rather static quenching. A hydrophobic attraction between the fluorophore and quencher can promote the formation of an intramolecular dimer, which i
