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Submit ReviewJanelia Fluor® 549, SE
Description: Yellow dye (Reactive group: NHS ester). Applications: super resolution microscopy e.g. dSTORM & STED, confocal, flow and live cell imaging
Alternative Names: JF 549, NHS
Chemical Name: 3,6-Di-1-azetidinyl-9-[2-carboxy-5-[[(2,5-dioxo-1-pyrrolidinyl)oxy]carbonyl]phenyl]xanthylium, inner salt
Biological Activity for Janelia Fluor® 549, SE
Janelia Fluor® 549, SE is a yellow fluorescent dye; supplied as an NHS ester for coupling to primary amine groups. NHS ester can be converted to relevant substrate for use in self-labeling tag systems, e.g. HaloTag® and SNAP-tag®. Suitable for confocal fluorescent imaging and super resolution microscopy (SRM) techniques, such as dSTORM (live and fixed cells) and STED. Also suitable for flow cytometry. Cell permeable. Excitation maximum = 549 nm; emission maximum = 571 nm; Quantum yield = 0.88; Extinction coefficient = 101,000 M-1cm-1; A280 correction factor is 0.169.
Please see the protocol for further information on protein/antibody labeling and conjugation.
We also offer Janelia Fluor® conjugated antibodies and custom conjugation services with our sister company Novus Biologicals.
HaloTag is a trademark of Promega Corporation, and SNAP-tag is a trademark of New England BioLabs, Inc.
Scientific Data
Super-Resolution Microscopy
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Application of Janelia Fluor® Dyes in Cardiac Tissue. An adult pig heart tissue section, 10 μm thick, labelled with abs against SERCA2ATPase, exhibits the intricate structure of the sarcoplasmic reticulum. A super-resolution image (top), obtained by exploiting spontaneous photo-switching of JF549 (dSTORM), shows superior detail to the diffraction limited widefield image (bottom). Scale: 200 nm. Image kindly provided by Prof. Christian Soeller, University of Exeter; acquired by Alex Clowsley and Anna Meletiou.
Super-Resolution Microscopy
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Application of Janelia Fluor® Dyes in Cardiac Tissue. A single isolated Wistar rat cardiomyocyte stained against alpha -actinin, displaying its periodic structure localised at the ends of sarcomeres (Z-discs). Widefield fluorescence of JF549 (left), prior to illuminating with a 561 nm laser to induce photoswitching and produce a dSTORM super-resolution image (right). Scale: 1 μm. Image kindly provided by Prof. Christian Soeller, University of Exeter; acquired by Alex Clowsley and Anna Meletiou.
Fluorescence Imaging
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Application of Janelia Fluor® Dyes in Cardiac Tissue. Widefield fluorescence image of muscle tissue from an adult pig heart, displaying the distribution of collagen VI in the interstitial space between muscle cells. The sample was labelled with a primary ab against collagen VI and a secondary ab conjugated to JF549, SE. Scale: 50 μm. Image kindly provided by Prof. Christian Soeller, University of Exeter; acquired by Alex Clowsley and Anna Meletiou.
Licensing Information
Sold under license from the Howard Hughes Medical Institute, Janelia Research Campus
Optical Data for Janelia Fluor® 549, SE
| Emission Color | Yellow |
|---|---|
| Brightness | |
| λabs | 549 nm |
| λem | 571 nm |
| Extinction Coefficient (ε) | 101,000 M-1cm-1 |
| Quantum Yield (φ) | 0.88 |
| Closest Laser line | 532 nm |
| Reactive Group | NHS ester |
| Reactivity | Primary amines |
| Cell Permeable | Yes |
| Correction Factor 280 | 0.169 |
| Application | Confocal Microscopy, Super Resolution Microscopy, Flow Cytometry, dSTORM, STED Microscopy |
| Alternative For | Alexa Fluor® 546, Alexa Fluor® 555, BDY TMR-X, Atto 550, CF 555, TAMRA, Cyanine 3 |
Alexa Fluor® is a registered trademark of Molecular Probes, Inc, a Thermo Fisher Scientific Company.
Plan Your Experiments
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.
Spectral Viewer
Technical Data for Janelia Fluor® 549, SE
| M. Wt | 551.56 |
| Formula | C31H25N3O7 |
| Storage | Store at -20°C |
| CAS Number | 1811539-32-8 |
| PubChem ID | 124201856 |
| InChI Key | DWUIXAGWHCMXHN-UHFFFAOYSA-N |
| Smiles | O=C(ON1C(CCC1=O)=O)C2=CC=C(C([O-])=O)C(C(C3=CC=C(N4CCC4)C=C3O5)=C(C=C/6)C5=CC6=[N+]7CCC\7)=C2 |
The technical data provided above is for guidance only. For batch specific data refer to the Certificate of Analysis.
Tocris products are intended for laboratory research use only, unless stated otherwise.
Solubility Data for Janelia Fluor® 549, SE
| Solvent | Max Conc. mg/mL | Max Conc. mM | |
|---|---|---|---|
| Solubility | |||
| DMSO | 55.16 | 100 | |
| DMF | 55.16 | 100 |
Preparing Stock Solutions for Janelia Fluor® 549, SE
The following data is based on the product molecular weight 551.56. Batch specific molecular weights may vary from batch to batch due to the degree of hydration, which will affect the solvent volumes required to prepare stock solutions.
| Concentration / Solvent Volume / Mass | 1 mg | 5 mg | 10 mg |
|---|---|---|---|
| 1 mM | 1.81 mL | 9.07 mL | 18.13 mL |
| 5 mM | 0.36 mL | 1.81 mL | 3.63 mL |
| 10 mM | 0.18 mL | 0.91 mL | 1.81 mL |
| 50 mM | 0.04 mL | 0.18 mL | 0.36 mL |
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Product Datasheets for Janelia Fluor® 549, SE
References for Janelia Fluor® 549, SE
References are publications that support the biological activity of the product.
Grimm et al (2015) A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat.Methods 12 244 PMID: 25599551
Deng et al (2015) CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proc.Natl.Acad.Sci.USA. 112 11870 PMID: 26324940
Knight et al (2015) Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science 350 823 PMID: 26564855
Legant et al (2016) High-density three-dimensional localization microscopy across large volumes. Nat.Methods 13 359 PMID: 26950745
If you know of a relevant reference for Janelia Fluor® 549, SE, please let us know.
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8 Citations for Janelia Fluor® 549, SE
Citations are publications that use Tocris products. Selected citations for Janelia Fluor® 549, SE include:
Erin Osborne et al (2020) mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage. Development PMID: 34004918
Florian et al (2020) mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage. Development 147 PMID: 32541012
Daniel M et al (2021) Internalization of the Membrane Attack Complex Triggers NLRP3 Inflammasome Activation and IL-1β Secretion in Human Macrophages. Front Immunol 12 720655 PMID: 34650553
Dylan M et al (2021) Improved Methods for Single-Molecule Fluorescence In Situ Hybridization and Immunofluorescence in Caenorhabditis elegans Embryos. Curr Protoc 1 e299 PMID: 34826343
Juan S et al (2021) SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum. Nat Commun 12 4552 PMID: 34315878
James et al (2021) Precision of tissue patterning is controlled by dynamical properties of gene regulatory networks. Development 148 PMID: 33547135
Sheila S et al (2019) Visualizing Transcription Factor Binding on Mitotic Chromosomes Using Single-Molecule Live-Cell Imaging. Methods Mol Biol 2038 239-250 PMID: 31407289
Franka et al (2019) Detection and quantification of RNA decay intermediates using XRN1-resistant reporter transcripts. Nat Protoc 14 1603-1633 PMID: 31019309
Do you know of a great paper that uses Janelia Fluor® 549, SE from Tocris? Please let us know.
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Protocols for Janelia Fluor® 549, SE
The following protocol features additional information for the use of Janelia Fluor® 549, SE (Cat. No. 6147).
Literature in this Area
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Fluorescent Dyes and Probes Research Product Guide
This product guide provides a background to the use of Fluorescent Dyes and Probes, as well as a comprehensive list of our:
- Fluorescent Dyes, including dyes for flow cytometry
- Fluorescent Probes and Stains, including our new MitoBrilliantTM mitochondria stains
- Tissue Clearing Kits and Reagents
- Aptamer-based RNA Imaging Reagents
- Fluorescent Probes for Imaging Bacteria
- TSA VividTM Fluorophore Kits
- TSA Reagents for Enhancing IHC, ICC & FISH Signals