What is your recommended quencher to partner with long wavelength dyes such as Quasar and Pulsar dye labels?

The BHQ-2 dye is our preferred pairing for long wavelength dyes. This recommendation relates to the ease of manufacture over BHQ-3 labeled oligos, resulting in probes with excellent purity and performance characteristics.

To suit particular assay requirements we synthesize probes with the BHQ-3 dye as well. However, in the context of linear dual-labeled probes, the BHQ-2 dye is perfectly capable of quenching Quasar 670, Quasar 705, and Pulsar 650. These results may defy the FRET model of quenching and so we believe that static quenching is an important contributor as well. A ground state complex requires physical interaction between dyes, but this conformation is accommodated by the flexible tether of a single-stranded oligo. More information about the static quenching mechanism can be found in the following citations.

Choosing Reporter-Quencher Pairs for Efficient Quenching Through Formation of Intramolecular Dimers. Johansson, M.K. In Methods in Molecular Biology, v. 335; V.V. Didenko, Ed; Humana Press: Totowa, NJ, 2006; pp 17-29.

Intramolecular Dimers: A New Design Strategy for Fluorescence-Quenched Probes. Johansson, M.K.; Cook, R.M. Chem.--Eur. J. 2003, 9, 3466-3471. (This paper was also the subject of this issue's cover art)

Intramolecular Dimers: A New Strategy to Fluorescence Quenching in Dual-Labeled Oligonucleotide Probes. Johansson, M.K.; Fidder, H.; Dick, D.; Cook, R.M. J. Am. Chem. Soc. 2002, 124, 6950-6956.

FAQs