Fluorophores & Quenchers

Service Details of Fluorophores & Quenchers

Fluorophores

A fluorophore (or fluorochrome) is a fluorescent chemical compound that can absorb light at a specific wavelength (excitation) and subsequently re-emit light at a longer, lower-energy wavelength (emission). This process is called fluorescence.

FAM: The most common and classic green fluorescent dye. It is very bright and reliable. It is often used as the standard reporter for a single target or as the first channel in multi-target experiments.

FITC: The classic green fluorescent dye. It's one of the oldest and most widely used fluorophores. While it is bright, it can fade quickly (photobleach) and is sensitive to pH changes. It's often used in microscopy and antibody labeling.

Cy Dyes: This is a very popular family of synthetic dyes (e.g., Cy3, Cy5, Cy7). They are known for being very bright and stable. Each number indicates a specific color (Cy3 is green-yellow, Cy5 is red, Cy7 is near-infrared). They are extremely common in genomics and protein studies.

TAMRA: It is a bright, orange/red-emitting fluorescent dye. It is widely used as both a fluorophore and a quencher in various applications.

HEX: A yellow-green fluorescent dye. Its emission color is between FAM and TAMRA (another common dye). It is frequently used as a second reporter in multiplex assays.

JOE: Similar to HEX, JOE is another dye that emits in the yellow-green spectrum. It is often used interchangeably with or as an alternative to HEX.

ROX: A popular synthetic dye that emits light in the red region of the spectrum. Unlike other fluorophores used to detect specific DNA targets (like FAM or HEX), ROX is to act as an internal reference dye in quantitative PCR (qPCR).

TET: A green fluorescent dye, very similar to FAM but with a slightly longer wavelength. It can be used alongside FAM in experiments that require two close but distinct signals.

Alexa Fluor Dyes: A premier series of dyes invented by Molecular Probes (now Thermo Fisher Scientific). They are synthesized to be brighter, more stable, and less pH-sensitive than traditional dyes like FITC or TAMRA. Each dye (e.g., Alexa Fluor 488, Alexa 555, Alexa 647) is designed to match a specific laser line and is often a superior replacement for older dyes.

ATTO Dyes: A line of high-quality German-engineered dyes known for their exceptional purity and brightness. They are similar in quality to Alexa Fluor and Cy dyes and are often used as alternatives. They cover a very broad range of the light spectrum.

Quasar Dyes: A family of bright, stable dyes primarily used in qPCR and genetic analysis. They are designed to be excellent reporters for molecular beacons and other hydrolysis probes.

Quenchers

A quencher is a molecule that, upon coming very close to a fluorophore, reduces or eliminates (quenches) its fluorescence. Quenchers work by absorbing the energy from the excited fluorophore and dissipating it as heat (via a mechanism called Förster Resonance Energy Transfer, or FRET) or by simply blocking the excitation light.

BHQ: A series of advanced dark quenchers (e.g., BHQ-1, BHQ-2, BHQ-3). They are known for their excellent quenching efficiency across a wide range of wavelengths. Each number is optimized to quench a specific color of fluorophore (e.g., BHQ-1 for green/yellow dyes, BHQ-2 for orange/red dyes, BHQ-3 for far-red dyes).

MGB: The MGB moiety helps the probe bind more tightly and specifically to its DNA target. This allows for the use of shorter probes and improves discrimination of single-base changes. The quencher on an MGB probe is usually a non-fluorescent quencher like NFQ.

XEN: A newer type of quencher designed to be a efficient and stable alternative to BHQ dyes. It is a dark quencher that provides strong suppression of fluorescence across a similar range of colors.

BKHFQ: Double quencher validation proves that adding a second quencher makes the assay darker when it should be off and brighter when it should be on, leading to more accurate and trustworthy results, especially for challenging targets.

Eclipse: An "Eclipse probe" typically refers to a complete DNA probe system that uses a proprietary dark quencher. They are known for their very low background signal and high performance in qPCR.