Fluorescent Dyes

Fluorescent Dyes | Fluorescent Dyes Portfolio | Common Reactive Handles | Fluorescent Dyes Resources

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 Tocris.com.

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

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).

Maleimides

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:

(1) Cu(I)-catalyzed Azide-Alkyne Click Chemistry reaction (CuAAC)

The CuAAC reaction couples an alkyne with an azide (a [3+2] alkyne-azide cycloaddition) using copper as a catalyst, forming a stable 1,4-disubstituted 1,2,3-triazole-linked conjugate. Pros: the reaction is bioorthogonal, uses low molecular weight reactive handles, is highly selective, quick, quantitative and pH-insensitive. Cons: the cytotoxicity of the copper catalyst required for this reaction limits its use in living systems.

(2) Strain-promoted Azide-Alkyne Click Chemistry reaction (SPAAC) (copper-free)

The SPAAC reaction is another azide-alkyne cycloaddition that avoids the use of copper, by incorporating the triple bond into a cyclooctyne. The cyclooctyne, DBCO (dibenzocyclooctyne, also known as DIBAC) is commonly used as a reactive handle for this reaction because it provides relatively rapid reaction kinetics and good stability in aqueous buffers. Pros: this reaction is copper-free and non-cytotoxic. Cons: it requires incorporation of relatively large cyclooctyne group.

(3) Tetrazine ligation based on Inverse-Electron-Demand Diels-Alder (IEDDA) chemistry

The IEDDA reaction is the ultrafast cycloaddition between a strained double bond (commonly trans-cyclooctene) and a labeled tetrazine. Pros: the reaction is bioorthogonal, compatible with living systems, very rapid reaction kinetics, no catalyst required, ‘turn-on’ fluorescence of the tetrazine-functionalized dyes upon conjugation. Cons: it requires incorporation of two relatively large reactive handles.

Novus Custom Conjugation Service

For pre-conjugated options, we also offer Janelia Fluor conjugated antibodies and custom conjugation services through our sister brand, Novus Biologicals.

Our Conjugation Services

Spectra Viewer

Use our spectra viewer to interactively plan your experiments, assessing multiplexing options. View the excitation and emission spectra for our fluorescent dye range and other commonly used dyes.

View Excitation & Emission Spectra