Janelia Fluor® Dyes

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Janelia Fluor® 549 Conjugated Antibodies

Janelia Fluor® 646 Conjugated Antibodies

Janelia Fluor® Reactive Dyes

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Originally developed at the Janelia Research Campus, the Janelia Fluor® dyes have recently been made commercially available conjugated to antibodies or supplied as NHS esters for custom labeling. These bright, photostable dyes enable sensitive detection of cellular targets in IHC, ICC, and flow cytometry applications and are especially suited for live-cell imaging.

Tomm20 JF 646 Confocal Image JF 646 Excitation and Emission Spectra

Z-stack confocal images (top panel) with SRRF (super-resolution radial fluctuations) analysis (bottom) of Tomm20, an outer mitochondrial membrane protein, in HeLa cells. Tomm20 was detected in HeLa cells using 1 µg/ml Rb anti-Tomm20 (NBP1-81556) and 1:500 JF646-conjugated anti-Rb secondary antibody (red). Cells were counterstained with Dapi (blue). Scale bar: 10 μm. Experiment run by Jill Jenkins and images acquired at the Advanced Light Microscopy Core Facility, University of Colorado.

A single isolated Wistar rat cardiomyocyte stained against α-actinin, displaying its periodic structure localized at the ends of sarcomeres (Z-discs). Widefield fluorescence of JF549 (left panel), prior to illuminating with a 561 nm laser to induce photoswitching and produce a dSTORM super-resolution image (right). Scale bar: 1 μm. Images kindly provided by Prof. Christian Soeller, University of Exeter, acquired by Alex Clowsley and Anna Meletiou.

What Researchers are Saying about Janelia Fluor® Conjugates

"We have been using the JF secondary antibodies and like them a lot for IHC. As advertised, they seem to be at least a little brighter and more photostable than the Alexa 647 and Cy3 dyes we had been using. We will probably switch over to these completely going forward."
- Steve Stowers, PhD, Assistant Professor, Montana State University

alpha-Smooth Muscle Actin Antibody Janelia Fluor 549
"It’s a great antibody and great fluorophore by its signal sharpness and photo stability."
- Anonymous

alpha-Smooth Muscle Actin Antibody [Janelia Fluor® 549]


Human tonsil stained for aSMA (red) and counterstained with DAPI (blue).

Find Janelia Fluor® conjugated antibodies from Novus and Janelia Fluor® reactive dyes from Tocris.

Benefits of the Janelia Fluor® dyes:

  • Bright and Photostable Dyes. Janelia Fluor® dyes have been specifically engineered to improve the brightness, fluorescence lifetime, and quantum yield of fluorescent dyes. Compared to Cy3 and TMR, Janelia Fluor® 549 is 2x brighter in vitro and in live-cell experiments.
  • Multicolor Detection and Analysis. The narrow emission spectra of Janelia Fluor® dyes enables combining multiple fluorescent labels to detect numerous cellular targets in a single tissue or cell sample.
  • Live-Cell Imaging of Intracellular Targets. Unlike most small organic fluorophores, Janelia Fluor® dyes are cell permeable. In addition, JF dyes are compatible with self-labeling systems such as HaloTag and SNAP-Tag, facilitating visualization and single molecule-tracking of intracellular targets in live cells.
  • Super Resolution Microscopy (SRM). Janelia Fluor® dyes are particularly useful for microscopy techniques including dSTORM (direct stochastic optical reconstruction microscopy) and STED (stimulated emission depletion).

Janelia Fluor® 549 (JF 549)

JF 549 Excitation and Emission Spectra
Emission Color Yellow
Brightness JF 549
Excitation max (nm) 549
Emission max (nm) 571
Extinction coefficient (ε, M-1cm-1) 101,000
Quantum yield (ф) 0.88
Common Equivalent Dyes Alexa Fluor 546, Alexa Fluor 555, Cy3, TRITC

Janelia Fluor® 646 (JF 646)

JF 646 Excitation and Emission Spectra
Emission Color Red
Brightness JF 646
Excitation max (nm) 646
Emission max (nm) 664
Max. extinction coefficient (ε, M-1cm-1) 152,000
Quantum yield (ф) 0.54
Common Equivalent Dyes Alexa Fluor 647, Atto 647, Cy5


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