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Modification : 3'-BHQ-3
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
| Catalog No | Scale | Price |
| 26-6473-05 | 50 nmol | $97.00 |
| 26-6473-02 | 200 nmol | $97.00 |
| 26-6473-01 | 1 umol | $320.00 |
| 26-6473-03 | 2 umol | $480.00 |
| 26-6473-10 | 10 umol | $2,561.00 |
| 26-6473-15 | 15 umol | $3,201.00 |
Black Hole Quencher-3 (BHQ-3) is classified as a dark quencher (a non-fluorescent chromophore), and is used as a 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 672 nm, and an effective absorbance range of 620-730 nm. BHQ-3, is chemically less stable, and degrades when exposed to oligo synthesis and deprotection conditions for long periods of time, such as when synthesizing or processing longer oligos. We recommend BBQ650, a dark quencher as an effective substitute. BBQ650 has an absorbance maximum of 650 nm, and an effective absorbance range of 550-750 nm (yellow to far red). It is chemically resistant to both oligonucleotide synthesis reagents, deblocking and deprotecting reagents that includes harsh chemicals, acid and ammonia solutions.
BBQ650.
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).
Click here for list of quenchers.
Click here for a list of fluorophores.
|
Quencher Spectral Data
|
|
Quencher
|
Absorption Max, nm
|
Quenching Range, nm
|
| Dabcyl |
453 |
380-530 |
| BHQ-0 |
495 |
430-520 |
| BHQ1 |
534 |
480-580 |
| BHQ2 |
579 |
550-650 |
| BHQ3 |
672 |
620-730 |
| BBQ-650 |
650 |
550-750 |
|
Click here for complete list of quenchers and details
|
**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, 3')
Oligo Purification