Quick Order |All Online Ordering|Product Catalog Ordering|Oligo Modifications List|Product Info & Literature|Oligo Design Tools/Resources

BBQ-650 NHS (Black Berry Quencher 650 NHS)


Code : [BBQ-650 N]

Search Modifications Modified Oligos Quick Price Estimate
picture of BBQ-650 NHS (Black Berry Quencher 650 NHS)

Modification : BBQ-650 NHS

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

[BBQ-650 N]

Catalog NoScalePrice
26-6734-0550 nmol$227.00
26-6734-02200 nmol$227.00
26-6734-011 umol$416.00
26-6734-032 umol$622.00
26-6734-065 umol$1,872.00

NHS modification is a post synthesis conjugation to a primary amino group thus an additional modification with an amino group is required. A C6 or C12 amino group can be placed at the 5' or for the 3' end a C3 or C7 amino and for internal positions an amino modified base is used, e.g Amino dT C6.

NHS based modifications are post synthesis conjugation performed using a primary amino group. The yield is lower as compared to direct automated coupling of modifications that are available as amidites. Approximate yield for various scales are given below.

~2 nmol final yield for 50 nmol scale synthesis.
~5 nmol final yield for 200 nmol scale synthesis.
~16 nmol final yield for 1 umol scale synthesis

BlackBerry Quencher 650 (BBQ650) is classified as a dark quencher (a non-fluorescent chromophore). Dark quenchers are extensively used as the 3-quencher moiety in a variety of Fluorescence Resonance Energy Transfer (FRET) DNA detection probes in which the fluorophore has a long wavelength (yellow to far red) emission maximum (e.g. Cy3, ROX, Cy5, Cy 5.5). Dark quenchers can serve in this role because they have long wavelength absorbance maxima. Dark quenchers 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).

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 (iodine, TCA) or deblocking solutions (ammonia, AMA). Consequently, for synthesis of longer oligos (> 50 bases), BBQ650 is the preferred quencher over BHQ-2 or BHQ-3, as the latter are chemically less stable, and degrade when exposed to oligo synthesis and deprotection conditions for long periods of time, such as when synthesizing or processing longer oligos.

Click here for list of quenchers.

Click here for a list of fluorophores.

Quencher Spectral Data


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."

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.
- BBQ-650 NHS (Black Berry Quencher 650 NHS)

Oligonucleotide Synthesis |  Flourescent Molecular Probes |  Gene Detection Systems |  Tools & Reagents |  Gene Assays |  RNAi
© 2024 Gene Link |  Terms & Conditions |  Licenses |  Privacy Policy |  June 19, 2024 6:44:16 AM