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Oligo Modifications List | Oligo Modifications Reference Category
Modification : Dabcyl-3
Reference Catalog Number 26-6470
Category Quenchers
Modification Code Dab
5 Prime Y
3 Prime Y
Internal Y
Molecular Weight (mw) 462.44
Extinction Coeficient (ec) 14.3
Technical Info (pdf) PS26-6470.pdf
Catalog NoScalePrice
26-6470-0550 nmol$147.50
26-6470-02200 nmol$147.50
26-6470-011 umol$191.75
26-6470-032 umol$282.62
26-6470-1010 umol$1,074.00
26-6470-1515 umol$1,217.50

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

Quencher

Absorption Max, nm

Quenching Range, nm

Dabcyl 453 380-530
BHQ1 534 480-580
BHQ2 579 550-650
BHQ3 672 620-730
BBQ-650 650 550-750
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.


References
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.

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