Cy®3 dye

Cy®3 dye is a bright, orange-fluorescent dye that can be excited using the 532 nm laser line and visualized with TRITC (tetramethylrhodamine) filter sets. In addition to immunocytochemistry applications, Cy®3 dye is commonly used to label nucleic acids.

The Cy®3 fluorophore is also the basis for the lipophilic neuronal and long-term DiI cell tracing reagents, which append alkyl tails (≥12 carbons) onto the core fluorophore.

Alexa Fluor® 555 dye is a Cy®3 dye alternative that is generally more fluorescent and more photostable than Cy®3 dye, making it well suited for applications such as imaging and flow cytometry.

Cy®3 dye dashboard

Initial brightness



The Cy®3 dye is a traditional orange-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 DiI and its variants.


Photostability in buffer


Photostability in antifade


  488/532 TRITC 554 568  
Laser line

Common filter set

Excitation max

Emission max

Cy®3 products

We offer a range of Cy®3 dye and DiI products including secondary antibodies, streptavidin conjugates, kits, and more. Learn more here:

Learn more about fluorescent dyes in the Cy®3 dye wavelength range

Cy®3-goat anti-rabbit

Double labeling of tubulin and HA-tagged tubulin in T. thermophila using Cy®3-goat anti-rabbit and FITC-goat anti-mouse.

High-performance alternatives to Cy®3 dye

Fluorescent conjugates

The Alexa Fluor® 555 dye—with nearly identical spectral properties to Cy®3 dye—produces brighter, more photostable conjugates. These conjugates are ideal for imaging and other applications requiring increased sensitivity and environmentally insensitive fluorescence detection.

We offer Alexa Fluor® 555 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.

Comparison of the relative fluorescence of goat anti–rabbit IgG antibody conjugates of Alexa Fluor® 555 and Cy®3 dyes (prepared in our laboratories) at different dye:protein ratios in the conjugate.


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®3 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.