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Short answer: Alexa Fluor 647 is a far-red fluorescent dye in the Thermo Fisher Alexa Fluor series, with a Handbook absorption maximum of about 650 nm and emission maximum of about 668 nm. It sits in the same optical channel as Cy5, and it is not visible to the human eye, so it is imaged with a far-red capable camera or detector.
What Alexa Fluor dyes are
Alexa Fluor is a trademarked family of fluorescent dyes from Molecular Probes (Thermo Fisher Scientific). The number is the nominal excitation wavelength, so Alexa Fluor 488 is excited near 488 nm. The dyes are sold as conjugates to antibodies, streptavidin, phalloidin and other probes, and are used in immunofluorescence, flow cytometry and microscopy. For the general concept, see the site’s guide to fluorophores.
Spectra and colour of the common Alexa Fluor dyes
The table gives the conjugate absorption and emission maxima and the colour from the Molecular Probes Handbook, with the spectrally similar Cy dye the Handbook lists as replaceable by the Alexa Fluor dye (Thermo Fisher, read 2026-11-07).
| Dye | Absorption / emission (nm) | Colour | Cy dye it can replace |
|---|---|---|---|
| Alexa Fluor 488 | 495 / 519 | Green | Cy2 (or fluorescein/FITC) |
| Alexa Fluor 555 | 555 / 565 | Orange | Cy3 (or TRITC) |
| Alexa Fluor 594 | 590 / 617 | Red | Texas Red (no Cy dye listed) |
| Alexa Fluor 647 | 650 / 668 | Far-red | Cy5 |
| Oregon Green 488 | 496 / 524 | Not given | Not listed |
Other Thermo Fisher pages round the same dye slightly differently (for example 650/665 or 650/670, and 651/672 for the free acid), so spectra depend on the source and the form of the dye. Treat the numbers as nominal and take filter choices from the data sheet for your conjugate and from your filter supplier: the Handbook table gives no filter values and refers readers to microscope makers and filter suppliers such as Chroma, Omega Optical and Semrock.
What colour does Alexa Fluor 488 emit?
Green. Alexa Fluor 488 emits at about 519 nm and is excited at about 495 nm, so it is read in the same channel as fluorescein-type dyes such as FITC. Oregon Green 488 has nearly identical Handbook values (496/524).
Is Alexa Fluor 647 red?
It is called far-red. The Handbook notes that the human eye cannot see far-red directly, so you cannot check the stain through the eyepiece. A detector or camera sensitive in the far-red is needed, and the image is displayed in a pseudocolour you assign. Alexa Fluor 594 (emission 617 nm) is the dye the Handbook labels red.
Is Alexa 555 the same as Cy3?
No. They are different molecules with similar optics. In a quantitative comparison, Berlier et al. (2003, J Histochem Cytochem 51:1699, PMID 14623938) found that as NHS esters Alexa Fluor 555 and Cy3 are similar, as are Alexa Fluor 647 and Cy5, in absorption and emission maxima, Stokes shift and extinction coefficient. The differences were in the conjugates: both Alexa dyes were significantly more resistant to photobleaching, Cy protein conjugates showed prominent blue-shifted shoulder peaks attributed to non-fluorescent dye aggregates, and Alexa 555 and 647 conjugates showed significantly less self-quenching, so were more fluorescent, especially at high degrees of labelling. The authors are Molecular Probes staff, so this is a manufacturer-authored comparison. The Handbook states that a swap usually needs no filter or instrument change.
What does Alexa Fluor mean?
It is the brand name of the dye family. The sources cited on this page do not state an origin for the name, so none is given here; the number is the nominal excitation wavelength in nanometres.
Where it matters in the lab
- Channel planning: assigning Alexa Fluor 488, 555 or 594, and 647 to separate channels spreads labels across the spectrum; see single-stain compensation controls for managing spillover in multicolour work.
- Instrument fit: a far-red dye needs a far-red capable detector; check the instrument configuration before choosing the 647 channel. An epifluorescence microscope needs a suitable filter set and camera.
- Photostability: the Handbook describes Alexa conjugates as brighter and more photostable than spectrally similar conjugates; see photobleaching and phototoxicity for the general problem.
- Super-resolution: the site’s STORM microscopy guide tabulates Alexa 647 photon counts and duty cycle.
Common misunderstandings
- “The number is the emission wavelength.” It is the nominal excitation wavelength; emission for 647 is near 668 nm.
- “Alexa 647 and Cy5 are interchangeable without checking.” They are spectrally similar but differ in photostability and self-quenching, so signal can differ at the same labelling.
- “I can see my far-red stain at the microscope.” The eye cannot see it; it needs a detector.
- “All sources agree on the peaks.” Values differ by a few nanometres between pages and forms.
FAQ
What color does Alexa Fluor 488 emit?
Green, with emission near 519 nm (Thermo Fisher Handbook).
Is Alexa 555 the same as Cy3?
No. It is spectrally similar but a different dye, with greater photostability and less self-quenching in conjugates (Berlier et al. 2003).
Is Alexa Fluor 647 red?
It is far-red (about 650 nm excitation, 668 nm emission) and is not visible by eye.
What does Alexa Fluor mean?
It is a trademarked dye family name; the cited sources give no etymology.
Sources
- Thermo Fisher Scientific, Molecular Probes Handbook, The Alexa Fluor Dye Series, read 2026-11-07.
- Thermo Fisher Scientific, Spectral characteristics and recommended bandpass filter sets, read 2026-11-07.
- Berlier JE et al. (2003) Quantitative comparison of long-wavelength Alexa Fluor dyes to Cy dyes. J Histochem Cytochem 51(12):1699-1712. doi:10.1177/002215540305101214, PMID 14623938, read 2026-11-07.
