Cy®5 dye

Cy®5 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 Cy®5 dye or Alexa Fluor® 647 dye over other fluorophores is the low autofluorescence of biological specimens in this region of the spectrum.

The Cy®5 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 Cy®5 dye in protein and nucleic acid conjugates. Allophycocyanin (APC) is another bright fluorophore that is spectrally equivalent to Cy®5 dye and Alexa Fluor® 647 dye, but it is used almost exclusively in flow cytometry.

Cy®5 dye

Initial brightness



Cy®5 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 Cy®5 649 666  
Laser line

Common filter set

Excitation max

Emission max

Cy®5 products

We offer a range of Cy®5 dye and DiD products including secondary antibodies, streptavidin conjugates, kits, and more. Learn more here:

Learn more about fluorescent dyes in the Cy®5 wavelength range

CellTracker™ CM-DiI

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

High-performance alternatives to Cy®5 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.

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 Cy®5 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 Cy®5 dye.


Molecular Probes® Handbook

Molecular Probes HandbookThe 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.


Antifade reagents

Antifade reagentsAntifade reagents suppress photobleaching and preserve the signals of your fluorescently labeled target molecules. They offer excellent compatibility with Cy®5 dye and a multitude of dyes across the spectrum, making them especially valuable tools for multicolor applications.

Cell stain tool

Cell stain toolStain 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.


Fluorescence SpectraViewer

Fluorescence SpectraviewerPlot and compare spectra and check the spectral compatibility for common fluorophores including all the Molecular Probes® fluorescent probes. The Fluorescence SpectraViewer tool is formatted for both microscope imaging and flow cytometry applications.