Janelia Fluor® 549, SE

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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
Datasheet
Citations (8)
Reviews
Protocols (1)
Literature (1)

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 Application of Janelia Fluor® Dyes in Cardiac Tissue View Larger

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 Application of Janelia Fluor® Dyes in Cardiac Tissue View Larger

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 Application of Janelia Fluor® Dyes in Cardiac Tissue View Larger

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

Janelia Fluor<sup>®</sup> 549, SE Dye Spectra
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

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.

Select a batch to recalculate based on the batch molecular weight:
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

Certificate of Analysis / Product Datasheet
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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.

Keywords: Janelia Fluor 549, SE, Janelia Fluor 549, SE supplier, JF549, Janelia, Fluor, 549,, SE, Fluorescent, dye, NHS, ester, self-labeling, tag, systems, microscopy, cell, permeable, super, resolution, STED, flow, cytometry, JF, Amine, Reactive, Dyes, Flow, Cytometry, 6147, Tocris Bioscience

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


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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

Tocris offers the following scientific literature in this area to showcase our products. We invite you to request* your copy today!

*Please note that Tocris will only send literature to established scientific business / institute addresses.


Fluorescent Dyes and Probes Research Product Guide

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
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