Oligo Labels – Fluorophores and Quenchers (FAM, ATTO™, Cy®)

Fluorophores and Quenchers

We are experienced in fluorescence and quencher modifications for oligonucleotide synthesis. As a result, we are able to offer our customers a wide range of high quality dyes and quenchers that enable highly accurate detection results.

The dyes that we use include ATTO™, Dyomics™, ELITech™, LI-COR® and many more.

In addition to these dyes, we also provide high-performance probes that are suitable for a range of molecular applications, such as quantitative real-time PCR (qPCR) and SNP detection. By partnering with us, you can be assured that your research projects will deliver reliable results.

An oligonucleotide label (oligo label) is a chemical tag attached to a short strand of DNA or RNA to make it visible or measurable. Labelling has many applications, such as tracking, detecting, or purifying nucleic acid sequences in laboratory experiments.

Oligonucleotide labels include fluorophores (light-emitting molecules), quenchers (molecules that reduce a nearby fluorophore’s signal by absorbing its excitation energy), and reporter–quencher pairs, such as those used in TaqMan® probes. They are also widely used in hybridization probes for the specific detection of nucleic acid sequences.

List of Fluorophores

Some of the most popular fluorophore options offered by ELLA Biotech are FAM (including 6-FAM), ATTO™ (e.g., ATTO 425, ATTO Rho101, ATTO Rho12 and ATTO 647N), Cy® dyes (e.g., Cy3, Cy5 and Cy5.5), HEX, JOE, ROX and Texas Red®.

Table 1. List of Fluorophores (with spectral characteristics and quantum yields). Values represent maximum absorption and emission wave lengths (λ), molar extinction coefficient (ε), quantum yield, correction factor at 260 nm (CF260) and brightness.

Quantum yield values indicate the number of emitted photons divided by number of absorbed photons. Extinction coefficient (ε) measures fluorophore’s ability to absorb light at a specific wavelength. Brightness represents total light output or visual intensity you can expect to see from a single molecule of the dye and is calculated by multiplying the dye’s extinction coefficient by its quantum yield.

* Please note that quantum yield and εmax (and thus brightness) depend on the solvent
** Please note that these are generica of Cy5 and Cy5.5 respectively

ATTO Fluorescent Labels And Dyes

List of Quenchers

Some of the most popular quencher options offered by ELLA Biotech are BHQ®, DABCYL, ELITech™, ATTO™.

Table 2. List of Quenchers (with spectral characteristics). Values represent maximum absorption and emission wave lengths (λ).

* TAMRA™ (em, max 580 nm) has some fluorescence in the visible wavelength

DDQ = Deep Dark Quencher
BHQ = Black Hole Quencher
BMN = Biomens
TQ = Tides Quencher
EDQ = Eclipse Dark Quencher

List of Reporter-Quencher Combinations

Reporter–quencher pairs are used in molecular biology and diagnostics to create “smart” fluorescent probes that emit a detectable signal when a specific genetic target is present, such as TaqMan® probes in qPCR, or Molecular Beacons.

Most common applications: qPCR TaqMan® Probes (e.g., FAM/BHQ® reporter–quencher combinations), Molecular Beacons, FRET assays, NGS, hybridization probes, Scorpion Probes, etc.

For applications requiring particularly low background fluorescence, double-quenched probes can be used. These probes contain a second quencher, typically added at the 9th position from the 5′ end, in addition to the primary quencher. The additional quencher can further reduce background fluorescence, particularly in longer oligonucleotides and probes labeled with high-energy fluorophores such as FAM.

Table 3. List of Reporter-Quencher Combinations (with spectral characteristics). Values represent maximum absorption and emission wave lengths (λ).

We also create custom Reporter-Quencher combinations on request.

Check out our page on hydrolysis and hybridization probes for qPCR and our Design Guide for Oligonucleotides with Multiple Modifications.