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BHQ-3 (Black Hole Quencher-3, 5')

picture of BHQ-3 (Black Hole Quencher-3, 5')

Modification : BHQ-3 (5')

Catalog Reference Number
Category
Modification Code
5 Prime
3 Prime
Internal
Molecular Weight (mw)
Extinction Coeficient (ec)
Technical Info (pdf)
Absorbance MAX
Emission MAX
Absorbance EC



26-6729
Quenchers
5'-BHQ-3
Y
N
N
597.63
8
PS26-6729.pdf
672
1
1


Catalog NoScalePrice
26-6729-0550 nmol$322.50
26-6729-02200 nmol$322.50
26-6729-011 umol$419.50
26-6729-032 umol$628.87
26-6729-1010 umol$3,356.00
26-6729-1515 umol$4,195.00

Black Hole Quencher-3 (BHQ-3) is classified as a dark quencher (a non-fluorescent chromophore), and is extensively used as the 3-quencher moiety in a variety of Fluorescence Resonance Energy Transfer (FRET) DNA detection probes. 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).

BHQ-3 has an absorbance maximum of 680 nm, and an effective absorbance range of 620-730 nm. It is the preferred quencher for pairing with fluorescent dyes that emit in the red-far red part of the visible range (640-775 nm). The emission spectra of this set of dyes sufficiently overlaps the absorbance spectrum of BHQ-3 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 License Agreement. ""Black Hole Quencher, BHQ, CAL Fluor and Quasar are registered trademarks of Biosearch Technologies, Inc., Petaluma, California. The BHQ, CAL Fluor and Quasar dye technologies are protected by U.S. and world-wide patents either issued or in application. Compounds incorporating these dyes are made and sold under agreement with Biosearch Technologies, Inc. for end-user's non-commercial research and development use only. Their use in commercial applications is encouraged but requires a separate Commercial Use License granted by Biosearch Technologies, Inc."



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.
- BHQ-3 (Black Hole Quencher-3, 5')

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