Janelia Fluor® 549, SE

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Description: Yellow dye (Reactive group: NHS ester). Application: flow cytometry, confocal microscopy, super resolution microscopy (SRM) including dSTORM & STED. Suitable for 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

Key Information: Janelia Fluor® 549, SE is a yellow fluorescent dye; supplied with an NHS ester reactive group for the labeling of primary amines. Suitable for live cell imaging.

Application: Suitable for flow cytometry, confocal microscopy, super resolution microscopy (SRM) including dSTORM and STED. Janelia Fluor® 549, SE is cell permeable.

Properties and Photophysical Data: NHS ester can be converted to relevant substrate for use in self-labeling tag systems, e.g. HaloTag® and SNAP-tag®. Excitation and emission maxima (λ) are 549 nm and 571 nm, respectively; quantum yield = 0.88; extinction coefficient = 101,000 M-1cm-1; A280 correction factor = 0.169; lactone-zwitterion equilibrium constant (KL-Z) = 3.5.

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, Flow Cytometry, Super Resolution Microscopy, dSTORM, STED
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

Zheng et al (2019) Rational design of fluorogenic and spontaneously blinking labels for super-resolution imaging. ACS Cent.Sci. 5 1602 PMID: 31572787


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:

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

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


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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

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