Color†	Absorb (nm)	Emit (nm)	MM (g/mol)	ε (cm−1M−1)	Quantum Yield Quantum yield The quantum yield of a radiation-induced process is the number of times that a defined event occurs per photon absorbed by the system. The "event" may represent a chemical reaction, for example the decomposition of a reactant molecule:...
Alexa Fluor 350	blue	346	442	410	19,000	-
— 405	violet	401	421	1028	34,000	-
— 430	green	434	541	702	16,000	-
— 488	cyan-green	495	519	643	71,000	0.92
— 500	green	502	525	700	71,000	-
— 514	green	517	542	714	80,000	-
— 532	green	532	554	721	81,000	0.61
— 546	yellow	556	573	1079	104,000	0.79
— 555	yellow-green	555	565	~1250	150,000	0.1
— 568	orange	578	603	792	91,300	0.69
— 594	orange-red	590	617	820	90,000	0.66
— 610	red	612	628	1172	138,000	-
— 633	red	632	647	~1200	100,000	-
— 647	red	650	665	~1300	239,000	0.33
— 660	red	663	690	~1100	132,000	0.37
— 680	red	679	702	~1150	184,000	0.36
— 700	red	702	723	~1400	192,000	0.25
— 750	red	749	775	~1300	240,000	0.12
† = approximate color of the emission spectrum ε = extinction coefficient

The Alexa Fluor family of fluorescent

Fluorescence

Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation of a different wavelength. It is a form of luminescence. In most cases, emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation...

 dyes is produced by Molecular Probes

Molecular Probes

Molecular Probes is a biotechnology company located in Eugene, Oregon specializing in fluorescence. The company was founded in 1975 by Richard and Rosaria Haugland in their kitchen in Minnesota, then moved briefly to Texas and finally to Oregon in the early 1980s. In 1989, Molecular Probes moved...

, a subsidiary

Subsidiary

A subsidiary company, subsidiary, or daughter company is a company that is completely or partly owned and wholly controlled by another company that owns more than half of the subsidiary's stock. The subsidiary can be a company, corporation, or limited liability company. In some cases it is a...

 of Invitrogen

Invitrogen

Invitrogen Corporation was a large, multinational biotechnology company headquartered in Carlsbad, California. In November 2008, a merger between Applied Biosystems and Invitrogen was finalized...

. Alexa Fluor dyes are typically used as cell and tissue labels in fluorescence microscopy

Fluorescence microscope

A fluorescence microscope is an optical microscope used to study properties of organic or inorganic substances using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption...

 and cell biology

Cell biology

Cell biology is a scientific discipline that studies cells – their physiological properties, their structure, the organelles they contain, interactions with their environment, their life cycle, division and death. This is done both on a microscopic and molecular level...

.

The excitation

Excited state

Excitation is an elevation in energy level above an arbitrary baseline energy state. In physics there is a specific technical definition for energy level which is often associated with an atom being excited to an excited state....

 and emission spectra of the Alexa Fluor series cover the visible spectrum

Visible spectrum

The visible spectrum is the portion of the electromagnetic spectrum that is visible to the human eye. Electromagnetic radiation in this range of wavelengths is called visible light or simply light. A typical human eye will respond to wavelengths from about 390 to 750 nm. In terms of...

 and extend into the infrared

Infrared

Infrared light is electromagnetic radiation with a wavelength longer than that of visible light, measured from the nominal edge of visible red light at 0.74 micrometres , and extending conventionally to 300 µm...

. The individual members of the family are numbered according roughly to their excitation maxima (in nm

Nanometre

A nanometre is a unit of length in the metric system, equal to one billionth of a metre. The name combines the SI prefix nano- with the parent unit name metre .The nanometre is often used to express dimensions on the atomic scale: the diameter...

).

Alexa Fluor dyes are synthesized

Chemical synthesis

In chemistry, chemical synthesis is purposeful execution of chemical reactions to get a product, or several products. This happens by physical and chemical manipulations usually involving one or more reactions...

 through sulfonation

Sulfonate

A sulfonate is a salt or ester of a sulfonic acid. It contains the functional group R-SO2O-.- Sulfonate salts:Anions with the general formula RSO2O− are called sulfonates. They are the conjugate bases of sulfonic acids with formula RSO2OH. As sulfonic acids tend to be strong acids, the...

 of coumarin

Coumarin

Coumarin is a fragrant chemical compound in the benzopyrone chemical class, found in many plants, notably in high concentration in the tonka bean , vanilla grass , sweet woodruff , mullein , sweet grass , cassia cinnamon and sweet clover...

, rhodamine

Rhodamine

Rhodamine is a family of related chemical compounds, fluorone dyes. Examples are Rhodamine 6G and Rhodamine B. They are used as a dye and as a dye laser gain medium. They are often used as a tracer dye within water to determine the rate and direction of flow and transport...

, xanthene

Xanthene

Xanthene is a yellow organic heterocyclic compound. Its chemical formula is 1310. It is soluble in diethyl ether. Its melting point is 101-102 °C and its boiling point is 310-312 °C...

 (such as fluorescein

Fluorescein

Fluorescein is a synthetic organic compound available as a dark orange/red powder soluble in water and alcohol. It is widely used as a fluorescent tracer for many applications....

), and cyanine

Cyanine

Cyanine is a non-systematic name of a synthetic dye family belonging to polymethine group. Cyanines have many uses as fluorescent dyes, particularly in biomedical imaging...

 dyes. Sulfonation makes Alexa Fluor dyes negatively charged

Electric charge

Electric charge is a physical property of matter that causes it to experience a force when near other electrically charged matter. Electric charge comes in two types, called positive and negative. Two positively charged substances, or objects, experience a mutual repulsive force, as do two...

 and hydrophilic. Alexa Fluor dyes are generally more stable, brighter, and less pH

PH

In chemistry, pH is a measure of the acidity or basicity of an aqueous solution. Pure water is said to be neutral, with a pH close to 7.0 at . Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline...

-sensitive than common dyes (e.g. fluorescein, rhodamine) of comparable excitation and emission, and to some extent the newer cyanine series. However, they are also more expensive. They are patented by Invitrogen (which acquired the company that developed the Alexa dyes, Molecular Probes).

History

The Alexa Fluor dyes were named after Alex Haugland, son of the founders of Molecular Probes, Richard and Rosaria Haugland. The Marina Blue dye was named after their daughter, Marina.

Comparison with other dyes

While extinction coefficients are known (see the table above), quantum yields and life times are not. Comparisons with other dyes should be considered depending on the conditions (technique) used and performance (signal, background, stability) needed.

The Alexa series dyes are less pH-sensitive and more photostable

Photobleaching

Photobleaching is the photochemical destruction of a fluorophore. In microscopy, photobleaching may complicate the observation of fluorescent molecules, since they will eventually be destroyed by the light exposure necessary to stimulate them into fluorescing...

 than the original dyes (fluorescein

Fluorescein

Fluorescein is a synthetic organic compound available as a dark orange/red powder soluble in water and alcohol. It is widely used as a fluorescent tracer for many applications....

, rhodamine

Rhodamine

Rhodamine is a family of related chemical compounds, fluorone dyes. Examples are Rhodamine 6G and Rhodamine B. They are used as a dye and as a dye laser gain medium. They are often used as a tracer dye within water to determine the rate and direction of flow and transport...

, etc.) from which they were synthesized. Brightness comparisons are also generally favorable. Comparisons with other dyes are less consistent, and also even more delicate, depending on the conditions (technique) used.
A third party has compared AlexaFluor647 with Cy5 (similar wavelength), conjugated to DNA. This study found that Cy5 is brighter, but less photostable than Alexa 647. Other providers claim better brightness of photostability (i.e. AlexaFluor488 compared to Dylight488) and Fluoprobes

Fluoprobes

The FluoProbes series of fluorescent dyes were developed by Interchim to improve performances of standard fluorophores. They are designed for labeling biomolecules, cells, tissues or beads in advanced fluorescent detection techniques....

488.
These findings have been both confirmed and contested in scientific literature marking the difficulty in quantitatively comparing dyes. AlexaFluors remain excellent dyes in many cases, but empirical testing

Empirical method

The empirical method is generally taken to mean the approach of using a collection of data to base a theory or derive a conclusion in science...

 is needed for optimal results in each application.

Similar lines of fluorescent dyes

Fluorophore

A fluorophore, in analogy to a chromophore, is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different wavelength...

 provide an alternative to the AlexaFluor Dyes (see also the list in :Category:Fluorescent dyes).

Applications

Labeled Nucleic acids

Quantification of nucleic acids

In molecular biology, quantitation of nucleic acids is commonly performed to determine the average concentrations of DNA or RNA present in a mixture, as well as their purity. Reactions that use nucleic acids often require particular amounts and purity for optimum performance...

 as well as labeled proteins

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

 are key features for multiple biological applications

Fluorescence in the life sciences

Fluorescence is used in the life sciences generally as a non-destructive way of tracking or analysing biological molecules by means of fluorescence....

. In most cases the amount of labeled sample is minimal and the labeling efficiency has to be quantified spectrophotometrically prior to the experiment. Specialized photometer, like the NanoPhotometer™, offer the possibility to determine the DNA, RNA or protein concentration of a sample as well as the incorporation of Alexa Flour dyes with submicroliter volumes (starting with 0.3 µl). In addition, due to the reduction of the optical pathlength with the NanoPhotometer™ samples are diluted automatically in comparison to standard cuvette measurements. The respective virtual dilution factors are considered by the software of the instrument. Because the measurements are processed with undiluted samples, the reproducibility of the results is very high and if desired, samples can be retrieved after the measurement for further processing.

External links

• Additional data table with molecular structures