Cy®5 dye

Invitrogen Cy5 dye is a bright, far-red-fluorescent dye with excitation ideally suited for the 633 nm or 647 nm laser lines. A significant advantage to using long wavelength dyes such as Cy5 dye or Invitrogen Alexa Fluor 647 dye over other fluorophores is the low autofluorescence of biological specimens in this region of the spectrum.

The Cy5 fluorophore is also the basis for the lipophilic neuronal and long-term DiD cell tracing reagents, which append alkyl tails (≥12 carbons) onto the core fluorophore.

For stable signal generation, Alexa Fluor 647 dye is generally brighter than Cy5 dye in protein and nucleic acid conjugates. Allophycocyanin (APC) is another bright fluorophore that is spectrally equivalent to Cy5 dye and Alexa Fluor 647 dye, but it is used almost exclusively in flow cytometry.

Cy5 dye

Initial brightness

Cy5 dye is a traditional far-red–fluorescent label for protein and nucleic acid conjugates used for imaging, flow cytometry, and genomic applications. It is also the basis for the classic lipophilic tracer DiD and its variants.  

Photostability in buffer


Photostability in antifade


  633/647 Cy5 649 666  
Laser line

Common filter set

Excitation max

Emission max

Cy5 products

We offer a range of Cy5 dye and DiD products including secondary antibodies, streptavidin conjugates, kits, and more. Learn more here:

Learn more about fluorescent dyes in the Cy5 wavelength range

See all Cyanine5 Primary Antibodies
See all Cyanine5 Secondary Antibodies


Brain of a zebrafish embryo stained with Invitrogen CellTracker CM-DiI prior to immunohistochemical analysis.

High-performance alternatives to Cy5 dye

Fluorescent conjugates

We offer Alexa Fluor 647 dye conjugated to a variety of antibodies, peptides, proteins, tracers, and amplification substrates optimized for cellular labeling and detection. In addition, reactive dye forms and protein labeling kits are available to allow you to generate your own antibody conjugates or probes.

Learn more about Alexa Fluor 647 dye

Allophycocyanin, also known as APC, is typically used for flow cytometry, microarrays, ELISA, and other applications that require either high sensitivity or simultaneous multicolor detection. We offer APC conjugated to a variety of primary and secondary antibodies for flow cytometry as well as tandem dye constructs for longer Stokes shift detection.

Comparison of the brightness of Alexa Fluor 647 and Cy5 dye antibody conjugates
Comparison of the brightness of Alexa Fluor 647 and Cy5 dye antibody conjugates (prepared in our laboratories). More Alexa Fluor 647 dye molecules can be attached to proteins and nucleic acids without significant quenching, thus yielding conjugates that are much brighter than those possible using the Cy5 dye.


Molecular Probes Handbook

Cell stain tool

The significantly revised 11th Edition is the most complete fluorescence labeling and detection reference available. The Molecular Probes Handbook can help you achieve the best experimental results for your fluorescence labeling and detection experiments. View the handbook online or order your own copy.

Go to the Handbook online
Order your copy of the Handbook

Antifade reagents

Cell stain tool

Antifade reagents suppress photobleaching and preserve the signals of your fluorescently labeled target molecules. They offer excellent compatibility with a multitude of dyes across the spectrum, making them especially valuable tools for multicolor applications. For added convenience, some formulations include the nuclear counterstain DAPI, eliminating the need for a separate counterstaining step.

See the performance of this dye in SlowFade Antifade reagents
See the performance of this dye in ProLong Antifade reagents

Cell stain tool

Cell stain tool

Stain your own cell by using our simulation tool to develop reproducible results with many of our signature fluorescent dyes. Develop your multiplexing strategy for antibody probes, reactive dyes, and counterstains to create your perfectly labeled fluorescent cell.

Go to the cell stain tool

Fluorescence SpectraViewer


Plot and compare spectra and check the spectral compatibility for common fluorophores including all of the fluorescent probes from Thermo Fisher Scientific. The Fluorescence SpectraViewer tool is formatted for both microscope imaging and flow cytometry applications.

Go to the Fluorescence SpectraViewer

Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.