Fluorescent molecules & fluorophore-conjugated antibodies

Advanced fluorophores and fluorescent-tagged proteins for multiplex imaging, flow cytometry, and immunodetection

Fluorescent molecules are essential tools in modern life science research, enabling sensitive detection, multiplex staining, and high-resolution visualization in applications including flow cytometry, fluorescence microscopy, immunohistochemistry (IHC), ELISA, and Western blotting. Fluorophore-conjugated secondary antibodies and fluorescent proteins provide researchers with exceptional flexibility for experimental panel design and quantitative imaging.

Jackson ImmunoResearch offers a comprehensive range of fluorescent dyes and fluorescent-tagged proteins spanning the visible to near-infrared spectrum. These fluorophores are optimized for compatibility with common excitation lasers and filter sets while delivering high brightness, photostability, and low background staining. Available conjugates include Alexa Fluor®, Cyanine (Cy™), Brilliant Violet™, FITC, DyLight™, APC, R-PE, PerCP, and additional fluorescent probe families.

Key features

Fluorescent secondary antibodies and protein conjugates provide several advantages over enzymatic or chromogenic detection systems:

• High sensitivity for low-abundance targets
• Multiplex capability for simultaneous detection of multiple analytes
• Quantitative signal measurement
• Broad compatibility with fluorescence microscopy and flow cytometry
• Flexible spectral selection for panel design
• Rapid imaging with minimal background interference

Fluorophores and fluorescent proteins used in bioimaging

The image illustrates two major classes of fluorescent probes employed in biological research. On the left, a stylized DNA double helix is labelled with fluorescent signals, representing the use of fluorophores to detect, track, and visualize nucleic acids and other biomolecules. On the right, a molecular structure shown in green represents a fluorescent protein, highlighting genetically encoded fluorescent markers that enable real-time imaging of cellular processes. Together, fluorophores and fluorescent proteins are essential tools for fluorescence microscopy, molecular labelling, and the study of biological structure and function at the cellular and molecular levels.

Fluorophores and fluorescent proteins

Fluorophores

Modern fluorophores are engineered to resist photobleaching and maintain fluorescence intensity under demanding experimental conditions.

Alexa Fluor® Dyes

Alexa Fluor® dyes are among the most widely used fluorescent dyes in biological imaging due to their brightness, photostability, and broad pH tolerance. They are suitable for microscopy, IHC, and flow cytometry applications

Find out more about the range of Alexa Fluor® available from Jackson ImmunoResearch.

Cyanine Dyes (Cy™ Dyes)

Cy™ fluorophores are widely used in fluorescence microscopy and imaging applications requiring compatibility with non-polar mounting media such as DPX or Permount™. Cyanine dyes can exhibit enhanced brightness under dehydrated mounting conditions compared with aqueous-compatible dyes.

Common cyanine fluorophores include Cy™2, Cy™3 and Cy™5, typically used for green fluorescence imaging, orange/yellow multiplex staining and far-red fluorescence detection, respectively.

Fluorescein Isothiocyanate (FITC)

FITC remains one of the most commonly used fluorophores in immunofluorescence and flow cytometry. Although less photostable than Alexa Fluor® dyes, FITC is cost-effective and compatible with many standard FITC-filter sets.  Due to it's fast photobleaching and lower brightness under prolonged imaging conditions, it is more suitable for applications not requiring ultra-high sensitivity.

Brilliant Violet™ Dyes

Brilliant Violet™ fluorophores are polymer-based dyes designed for high fluorescence intensity and improved sensitivity in flow cytometry applications. Brilliant Violet™421 and Brilliant Violet™480 are especially useful in high-parameter flow cytometry panels where bright signal intensity is required.

Aminomethylcoumarin Acetate (AMCA) 

AMCA is a blue-emitting fluorophore dye widely used due to its minimal fluorescence overlap with green- and other longer- wavelength-emitting fluorescent dyes.  Although it has lower brightness compared to newer fluorophores, it is still an ideal fluorescent molecule for multiplex staining and fluorescence microscopy due to the minimal spectral overlap.

Fluorescent proteins

Fluorescent proteins provide highly sensitive signal amplification and are commonly used for surface labelling in imaging and flow cytometry. Due to it's photolabile nature, signal fades rapidly in conventional epifluorescence and confocal microscopy, and therefore requires the use of an anti-fading mounting agent such as n-propyl gallate.

R-Phycoerythrin (R-PE)  

R-PE is a highly bright phycobiliprotein isolated from red algae and widely used in flow cytometry applications. It can be excited across a broad visible spectrum and provides intense orange fluorescence, making it an ideal fluorophore to use with low abundance targets.

Allophycocyanin (APC)

APC is a far-red fluorescent protein isolated from blue-green algae and commonly used in multicolour flow cytometry panels. It has reduced cellular autofluorescence and a strong far-red emission profile making it an excellent choice for multiplex compatability.

Peridinin-Chlorophyll-Protein (PerCP)

PerCP is a fluorescent protein complex primarily used in flow cytometry applications requiring 488 nm excitation with emission in the far-red region. It has a distinct spectral separation from FITC and PE making it useful for multicolour panel design.

Choosing the right fluorescent molecules

Selecting the optimal fluorescent molecule depends on your assay requirements

​Material available for download

Fluorophore selection and panel building blog

Alexa Fluor® fluorescent dyes are a trademark of Life Technologies Corp. They are provided under an agreement between Life Technologies Corp and Jackson ImmunoResearch Laboratories, Inc and the manufacture, use, sale, or import of these dyes is sold pursuant to a license from Life Technologies Corp for use of its fluorescent dye technology. The sale of these dyes or products containing these dyes is expressly conditioned on the buyer not using them (1) in manufacturing; (2) to provide a service, information, or data to an unaffiliated third party for payment; (3) for therapeutic, diagnostic, or prophylactic purposes; (4) to resell, sell, or otherwise transfer this product or its components to any third party, or for any other commercial purpose. For information on purchasing a license to this product for purposes other than research, contact Life Technologies Corp, 5791 Van Allen Way, Carlsbad, CA 92008 or outlicensing@lifetech.com.