What Are Fluorescent Dyes

What Are Fluorescent Dyes?

excitation moleculeWe had an interesting request to blog about the Fluorescent Dyes that are out on the market. Before we do that though, let’s get you up to speed on Fluorescent Dyes. One of our content writers studied chemistry in college and had this to say.

Most biological research laboratories depend on Fluorescent Dyes during standard tests that require the use of fluorescent molecules. The dyes are becoming more widely used as more people researching are finding just how versatile these fluorescent dyes can be in addition to their sensitivity levels and quantitative capabilities. These fluorescent probes have many uses in the lab, they can detect protein location and activation, and have the ability to identify complex protein formations, in addition to conformational changes and monitor advanced biological processes in vivo.

The real benefit of these fluorescent molecules (fluorophores/fluors) in the laboratory is that they have a unique reaction to light that passes through them when compared to other molecules. As the light passes through, it actually gets absorbed by an electron of a fluorescent particle. This then generates energy in the electron and propels it to an exited state. While this moment of excitation is happening, there is energy that begins to dissipate from a molecular collision and/or gets transferred to a proximal molecule, and the energy that remains then gets emitted as a photon which intern brings the electron back to a grounded state. Typically, the emitted photon will carry less energy, as a result it usually has a longer wavelength than the photon that experienced excitation, this allows the emitted fluorescence to be distinguished from the excitation light. The excitation produces an emission from the fluorophore that is cyclical, and until the the fluorophore is damaged beyond use, researchers can continue to excite the fluors until it reaches that stage. Because of this, the fluors can emit numerous photons repeatedly during this cycle of excitation, as a result the emissions and fluorescent molecules can continue to be used for a vast range of research.

Fluorophores can thus emit numerous photons through this cycle of excitation and emission and fluorescent molecules are therefore used for a broad range of research applications. You can learn in detail how fluorescent molecules work.




Fluorescent Dyes

diagram of Alexa Fluor 488

• Alexa Fluor 488 Dye

This dye is very bright, it is a fluorescent green dye that experiences excitation that is commonly suited to the 488 nm laser line. This dye is great for generating stable imaging and flow cytometry. It should also be noted that the Alexa Fluor 488 dye is pH-insensitive over a very wide molar range.

These probes that contain high fluorescence in addition to high photo stability are often times better for detecting a low-abundance of biological micro structures that illuminate with increased sensitivity. It’s common for Alexa Fluor 488 dye molecules to become attached to a protein molecule when exposed at high molar ratios without experiencing significant self-quenching. This can enable brighter conjugates, and and provide a more detailed detection.

• Cyanine Dyes

Cyanine dyes are specific molecules that contain a polymethine bridge between two unique nitrogen atoms that have a delocalized charge. As the result of this structure, cyanine dyes are known to have incredibly high extinction coefficients. There are different substituents that allow for the control of these properties, those most commonly being absorbance wavelength, photo stability, and fluoros.

• IR Fluors
“Bright, photostable and hydrophilic near-IR dye that is spectrally similar to Alexa Fluor® 750 and Cy7® Dye.

Bright and hydrophilic, far-red-fluorescent dye excited by the 633 nm or 647 nm laser lines.”

• MB Dyes

M.B. Dyes Chemical & Silk Ind. (Pvt.) Ltd. is a manufacturer of diversified auxiliary chemicals and dyes/pigments for Textile, Leather and Paint Industries. We also deal with many raw materiel used in these industries. We produced gamut of these chemicals for customer convenience to lessen their worries regarding raw material regular supply from a single source. Our manufacturing unit is located in Gadoon Amazai Industrial Estate Swabi NWFP and producing more than 110 products.

• Classic Fluorescent Dyes

What’s a fluorescent probe? It is a fluorophore that has been designed to localize in an isolated region of a biological specimen or to react to a specified stimulus. The Fluroprobes are fluorescent and give researchers the ability to identify specific components of complex bio-molecular structures that include living cells. The dyes have also been used regularly to modify things like amino acids, peptides, proteins, carbs, and other bio-molecules.

About Fluorophore
From Wiki: https://en.wikipedia.org/wiki/Fluorophore

“A fluorophore (or fluorochrome, similarly to a chromophore) is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with several π bonds.

Fluorophores are sometimes used alone, as a tracer in fluids, as a dye for staining of certain structures, as a substrate of enzymes, or as a probe or indicator (when its fluorescence is affected by environmental aspects such as polarity or ions). More generally they are covalently bonded to a macromolecule, serving as a marker (or dye, or tag, or reporter) for affine or bioactive reagents (antibodies, peptides, nucleic acids). Fluorophores are notably used to stain tissues, cells, or materials in a variety of analytical methods, i.e., fluorescent imaging and spectroscopy.

Fluorescein, by its amine reactive isothiocyanate derivative FITC, has been one of the most popular fluorophores. From antibody labeling, the applications have spread to nucleic acids thanks to (FAM (Carboxyfluorescein), TET,…). Other historically common fluorophores are derivatives of rhodamine (TRITC), coumarin, and cyanine. Newer generations of fluorophores, many of which are proprietary, often perform better, being more photostable, brighter, and/or less pH-sensitive than traditional dyes with comparable excitation and emission.”