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Fluorescent Dyes

Our range of fluorescent dyes includes the Janelia Fluor® Dyes, which provide scientists with an exceptional palette of bright, photostable fluorophores for a broad range of applications, including super-resolution microscopy. The Janelia Fluor range includes products that possess different specific and useful properties, such as: fluorogenicity; spontaneous blinking (for facile single-molecule localization microscopy, SMLM); and photoactivation. Our Photoactivable Janelia Fluor® Dyes are particularly useful for Photoactivated Localization Microscopy (PALM) imaging. Also included in our portfolio are novel fluorophores in the near-infrared range, for deep tissue and in vivo imaging work. Together with a comprehensive palette of gold-standard dyes, we have products for all your imaging requirements.

Fluorescent dyes with a range of reactive handles are available to easily label various biomolecules. Common reactive groups include: succinimidyl esters (SE / NHS esters); maleimides; free acids; and click handle groups. Click handles include tetrazine, DBCO and azide handles to support copper-free, bioorthogonal click chemistry, and azide / alkyne handles to support copper-catalyzed click chemistry. 

Protocols for fluorescent dyes conjugation are provided at

More information about Common Reactive Handles is provided below.

Fluorescent Dyes Portfolio

Product Name Reactive Group Cat. No. Excitation Wavelength (nm) Emission Wavelength (nm) Brightness Emission Color
Ocean Blue NHS ester 6489 405 455 3 Blue
BDY FL NHS ester 5465 502 510 4 Green
FITC Isothiocyanate 5440 495 525 3 Green
Janelia Fluor® 525 NHS ester 6296 525 549 5 Yellow
HM Janelia Fluor® 526 NHS ester 7312 526 550 - Yellow
Janelia Fluor® 526 NHS ester 7316 526 550 5 Yellow
PA Janelia Fluor® 549 NHS ester 6149 551-553 570-573 - Yellow
Janelia Fluor® 549 Maleimide 6500 549 571 5 Yellow
Tetrazine 6502 549 571 5 Yellow
NHS ester 6147 549 571 5 Yellow
Free acid 6503 549 571 5 Yellow
Janelia Fluor® 585 NHS ester 6418 585 609 5 Orange/Red
Janelia Fluor® 635 NHS ester 6419 635 652 5 Orange/Red
PA Janelia Fluor® 646 NHS ester 6150 649-651 663-665 - Orange/Red
Janelia Fluor® 646 Maleimide 6590 646 664 4 Orange/Red
Free acid 6993 646 664 4 Orange/Red
Azide 7088 646 664 4 Orange/Red
Tetrazine 7279 646 664 4 Orange/Red
NHS ester 6148 646 664 4 Orange/Red
5-TAMRA  NHS ester 7665 546 580 3 Orange/Red
Cyanine 5 NHS ester 5436 649 666 3 Orange/Red
SMCy 5.5 Alkyne 7295 636 660 5 Far red 
Janelia Fluor® 669 NHS ester 6420 669 682 3 Far red 
FNIR-Tag NHS ester 7373 765 788 4 Near-IR
NIR Dye s775z NHS ester 7626 775 795 3 Near-IR
Indocyanine green - 7510 787 815 3 Near-IR
ICG-d7 - 7749 794 818 3 Near-IR
Emission Colour Graphic

Common Reactive Handles

Chemistry reaction of fluorescent dyes with common Reactive handles

Succinimidyl Esters (SE / NHS esters)

NHS ester derivatives are suitable for modifying primary amines, which are prevalent on the surface of antibodies and other proteins due to the lysine side chain. Typically, NHS ester conjugation reactions are performed at slightly alkaline pH (pH=8-8.5).

Chemistry reaction of fluorescent dyes with common Reactive handles


Maleimides react with thiols (sulfhydryl groups), and so provide a convenient route to label cysteine-residues in proteins and peptides.

Free Acids

Free acid reactive groups are commonly used in the preparation of Halo- and SNAP-tag ligands via amide coupling reactions.

Click Handle groups

Click Chemistry refers to a class of chemical reactions that are modular, high yielding and simple to perform and purify. Click chemistry is therefore highly attractive as an approach for bioconjugation (attachment of a substrate of interest to a specific biomolecule), particularly site-specific bioconjugation. Highly related to the concept of click chemistry is ‘bioorthogonal chemistry’, which refers to reactions that can occur in biological environments without interfering with biochemical processes. The development of click chemistry and bioorthogonal chemistry was the subject of the 2022 Nobel Prize in Chemistry. The most common click chemistry reactions used for bioconjugation are summarized below:

Fluorescent Dyes Resources

Fluorescent Probes and Dyes Brochure from Tocris

Fluorescent Dyes and Probes Brochure

This product guide showcases our range and gives background on the use of Fluorescent Dyes and Probes. 

Flow cytometry handbook

Flow Cytometry Handbook

Explore a Step-By-Step Guide to Flow Cytometry.

Immunohistochemistry (IHC) Handbook from BioTechne

Immunohistochemistry (IHC) Handbook

This recently updated handbook offers a comprehensive introduction to IHC.