Fluorescent dyes
 

You can find a list of all fluorescent dyes available at biomers.net here. 

In addition to the wide range of known fluorescent dyes, biomers.net also offers its own excellent alternatives. The so-called BMN dyes can be attached to an oligonucleotide at the 5´- or 3´-end.

* Due to the changed patent situation of the cyanines, we recommend the use of the analog cyanine dyes Cyanine 5 (analog BMN-5) and Cyanine 5.5 (analog BMN-6). 

In addition to this wide range of available quenchers, biomers.net also offers a "proprietary" quencher set.
The BMN quenchers of biomers.net are excellent alternatives to the traditional Dark Quenchers due to their optimal matching quenching range. 

                              

Figure1: dT20 oligo with 3´-quencher, meaurement of absorption spectra in buffer (pH 7.0) 

BMN-Q460

With an absorption maximum of 460 nm, our Dark Quencher BMN-Q460 is particularly suitable for the short-wavelength region and represents an excellent alternative for the quenchers Dabcyl and DDQ I.
In addition to use in Molecular Beacons, in which it inhibits fluorescent signals by contact-quenching, BMN-Q460 can be used in various molecular biological applications. As 3´-quencher in Dual-Labelled probes (5´-nuclease assay), BMN-Q460 can be used in the range of 400-530 nm, so it is ideally suited for the fluorophores Atto 390, Atto 425 and Atto 465.
biomers.net offers the quencher BMN-Q460 as 5´-, 3´- or internal modification. 
 

BMN-Q535

BMN-Q535 is the second Dark Quencher of biomers.net and has an absorption maximum at about 535 nm and a quenching range from about 480 nm to 580 nm. This is the same range as BHQ-1, TQ2, DDQ I, Eclipse-Quencher or Iowa Black FQ, so BMN-Q535 may be an excellent alternative for this quenching.
BMN-Q535 is used as 3'-modification for standard Dual-Labelled Probes and Molecular Beacons.
We offer this quencher as 5 'or 3 modification. In addition, BMN-Q535 can be used as internal modification in Double Quenched probes with increased sensitivity.
 

Dual-Labelled Probe	Double Quenched Probe	Molecular Beacon Probe

BMN-Q1 und BMN-Q2

BMN-Q1 and BMN-Q2 are direct alternatives with identical specifications to BHQ-1 and BHQ-2.

BMN-Q620

Similar to the quenchers BMN-Q460 and BMN-Q535, biomers.net also offers the dark quencher BMN-Q620 as
5´, 3´ and internal modification. Thus, BMN-Q620 can be used ideally in Double Quenched Probes for the longer wavelength region. With an absorption maximum of 620 nm and a quenching range of 480 nm to 720 nm, it has a relatively wide range and can therefore optimally quench fluorescence dyes also in the long-wave range, e.g. Cyanine 5 or Cyanine 5.5.


BMN-Q651

With an absorption maximum at 650 nm and a quenching range of 550-720 nm, the biomers.net quencher BMN-Q651 optimally covers the longer wavelength range. BMN-Q651 can be used as an alternative to BBQ-650 or DDQ II. 

Quenchers can absorb energy that is dissipated by a fluorophore and emit it either as light of a longer wavelength (FRET quenching) or as heat. 
The most commonly used quenchers are Dabcyl (4,4-Dimethylaminoazobenzene-4-carboxylic acid) and Tamra, a fluorescent dye. According to the fact that Tamra is a fluorophore by itself, it can be cause of high background fluorescence. Increasingly, therefore non-fluorescent quencher, so-called Dark Quenchers, have established.
In contrast, Dark Quenchers are molecules that can absorb energy emitted by fluorophores without showing any fluorescence by themselves.

                         

Figure 1: Comparison of amplification curves (normalized) of a qPCR assay with 5'-6-Fam-labeled probes and four different 3'-quenchers.
In each assay, the same primer and probe sequences were used. All assays were run in duplicate (Genaxxon ProbeMasterMix No ROX,
MyGo Pro, pre-calibrated channel for Fam).
In direct comparison, the quenchers (BMN-Q535, BMN-Q620, BHQ-1 and TQ2) show almost identical results with the fluorescence dye 6-Fam. 


It is important that fluorophore and quencher are compatible with each other. The individual quenchers offered by biomers.net differ in their absorption maxima. The quenching efficiency of the quencher peaks in its absorption maximum. Therefore one can and should select the appropriate quencher for a certain dye. 

biomers.net bietet eine Auswahl von Dark Quenchern, die nahezu den gesamten Farbstoff-Bereich abdecken:




BMN Quencher (BMN-Q460, BMN-Q535, BMN-Q1, BMN-Q620, BMN-Q2, BMN-Q651):
Our biomers.net quencher set containing the quenchers BMN-Q460, BMN-Q535, BMN-Q1, BMN-Q620, BMN-Q2 and BMN-Q651, nearly covers the complete wavelength range. 
All BMN quenchers are produced by biomers.net. 
With an absorption maximum of 460 nm, our Dark Quencher BMN-Q460 is particularly suitable for the short-wavelength region and represent an excellent alternative for the quenchers Dabcyl and DDQ I.
In addition to use in Molecular Beacons, in which it inhibits fluorescent signals by contact-quenching, BMN-Q460 can be used in various molecular biological applications. As 3´-quencher in Dual-Labelled probes (5´-nuclease assay), BMN-Q460 can be used in the range of 400-530 nm, so it is ideally suited for the fluorophores Atto 390, Atto 425 and Atto 465.
BMN-Q535 is a Dark Quencher with an absorption maximum at about 535 nm and a quenching range from 480 nm to 580 nm. The quencher is in the same range as BHQ-1 and according to this BMN-Q535 can be used as excellent alternative to this quencher.
A perfect alternative to BHQ-1 is our quencher BMN-Q1, which has the same characteristics as the Black Hole Quencher. Like BMN-Q535, BMN-Q1 has an absorption maximum of about 535 nm and a quenching range of about 480 to 580 nm. 
With its absorption maximum at approx. 580 nm and a quenching range of 500 to 650 nm, BMN-Q2 has the same properties as the quencher BHQ-2.
Further representatives from our biomers.net quencher set are BMN-Q620 and BMN-Q651. With an absorption maximum of 620 nm and a quenching range of 480-720 nm BMN-Q620 has a relatively wide range and can be efficiently used for a variety of fluorescent dyes. 
BMN-Q651 has a quenching range of 550-720 nm and an absorption maximum of 650 nm and thus ideally covers the long-wavelength region and can be used as an alternative to BBQ-650 or DDQ II.
 

Tide Quencher (TQ2, TQ3): Tide Quenchers (TQ) were designed and developed by AAT Bioquest and are license-free. These quenchers show a similarly good efficiency as Black Hole Quenchers. TQ2 (absorption maximum at 515 nm) fits quite perfect to 6-Fam and is also suitable for Sima, Hex, Tet and Joe.
TQ3 (absorption maximum at 570 nm) is highly compatible for quenching dyes like Cyanine 3 (Cy3) and Tamra, but also shows quenching activity in the longer wave area for Rox, Texas Red, California Red and Cyanine 3.5 (Cy3.5).
 

Black Hole Quencher (BHQ-1, BHQ-2): The Black Hole Quenchers (BHQ) were developed by Biosearch Technologies. One quencher is BHQ-1 with an absorption maximum at about 530 nm and a quenching range from 480 nm to 580 nm. Another one is BHQ-2 with a maximum of absorption at about 580 nm and a quenching range from 550 nm to 670 nm. Due to chemical instability of their building blocks, we do not offer oligonucleotides with BHQ-0 or BHQ-3. BHQ-2 is also suitable for the combination with Cyanine 5 (Cy5). 
 

Deep Dark Quencher (DDQ I, DDQ II): DDQ I and DDQ II were developed by the group of Tom Brown, Southampton and are license-free. Based on Methyl Red, DDQ I has an absorption maximum at about 470 nm. The other one, DDQ II, is based on Disperse Blue 3 and shows an absorption maximum at about 650 nm. 
Please note the modification DDQ II has been discontinued; it will be sold while stocks last. As an alternative to DDQ II, the biomers.net Quencher BMN-Q620 can be used. 
 

BlackBerry Quencher 650 (BBQ-650): BBQ-650, designed by Berry & Associates, is particularly well suited for longer wavelength absorbing dyes (e.g. Cyanine 5, Cyanine 5.5 etc.).