Modification : Dabcyl-3'
Catalog Reference Number
Molecular Weight (mw)
Extinction Coeficient (ec)
Technical Info (pdf)
Dabcyl-3' is classified as a dark quencher (a non-fluorescent chromophore), and is typically used to label a Fluorescence Resonance Energy Transfer (FRET) DNA oligonucleotide probe with a quencher moiety at the 3'-end. Such probes are primarily used in nucleic acid assays, but also find a place in nucleic acid structural studies (1). Examples include TaqMan probes (2), Scorpion primers (3), and Molecular Beacons (4).
Dabcyl-3' has an absorbance maximum of 479 nm, and an effective absorbance range of 346-489 nm. It is the preferred quencher for pairing with fluorescent dyes that emit in the blue to green part of the visible range (442-506 nm).
The emission spectra of this set of dyes sufficiently overlaps the absorbance spectrum of Dabcyl to allow the latter to quench the fluorescence of the former with a high degree of efficiency.
The advantages of using a dark quencher in a FRET probe are (a) low background fluorescence (and thus better signal-to-noise ratio), (b) higher dynamic range, (c) amenability to multiplex assays (due to a dark quencher having no secondary fluorescence), and (d) ease of synthesis of FRET probes with a dark quencher (due to dark quenchers being resistant to degradation during the oligo deprotection step) (5).
Quencher Spectral Data
Absorption Max, nm
Quenching Range, nm
Click here for complete list of quenchers
**Black Hole Quencher License Agreement
"Black Hole Quencher", "BHQ-1", "BHQ-2" and "BHQ-3" are registered trademarks of Biosearch Technologies, Inc., Novato, CA. The BHQ technology is licensed and sold under agreement with Biosearch and these products are sold exclusively for R&D use by the purchaser. They may not be used for clinical or diagnostic purposes and they may not be resold,
distributed or re-packaged.
1. Didenko, V.V. DNA Probes Using Fluorescence Resonance Energy Transfer (FRET): Designs and Applications. Biotechniques (2001), 31: 1106-1121.
2. Livak, K.J., Flood, S.J.A., Marmaro, J., Giusti, W., Deetz, K. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization.PCR Methods Appl. (1995), 4: 1-6.
3. Thelwell, N., Millington, S., Solinas, A., Booth, J., Brown, T. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. (2000), 28: 3752-3761.
4. Tyagi, S., Kramer, F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. (1996), 14: 303-308.
5. Yeung, A.T., Holloway, B.P., Adams, P.S., Shipley, G.L. Evaluation of dual-labeled fluorescent DNA probe purity versus performance in real-time PCR. Biotechniques. (2004), 36: 266-270, 272, 274-275.
- Dabcyl Quencher-3'