Janelia Fluor® 549, free acid

Technical documents: SDS CoA Datasheet

Product overview

Name Janelia Fluor® 549, free acid
Biological description

Cell-permeable, yellow fluorescent dye supplied as free acid. Used for the synthesis of Janelia Fluor® HaloTag® and SNAP-Tag® ligands for use in live cell imaging experiments (Grimm et al 2017) . Also suitable for flow cytometry. Janelia Fluor® 549 is 2 x brighter than TMR and Cy3 in vitro and live-cell experiments.

Spectrally similar dyes: Alexa Fluor® 546, Alexa Fluor® 555, BDY TMR-X, Atto 550, CF 555, TAMRA, Cyanine 3

Alternative names JF549, free acid

Yellow dye supplied as a free acid. Suitable for dSTORM, STED, confocal microscopy, live cell imaging and flow cytometry.

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Fig1. Excitation and emission spectra of Janelia Fluor ® 549, free acid.

Figure1. Excitation and emission spectra of Janelia Fluor® 549, free acid. Janelia Fluor® 549 is a yellow fluorescent dye suitable for confocal and super resolution microscopy. A 1 µM solution was prepared in PBS before excitation, emission and absorbance spectra were generated. For protocol see #Protocol 1 in application notes below.

Optical Data

Emission color Yellow
Max excitation wavelength 549 nm
Max emission wavelength 571 nm
Quantum Yield (φ) 0.88
Extinction Coefficient (ε) 101,000 M-1cm-1
Cell permeable Yes
Reactive Group Free acid

Biological Data

Application notes

#Protocol 1: Measurement of excitation and emission spectra of Janelia Fluor ® 549, free acid

  • Janelia Fluor® 549, free acid was prepared at 1µm in PBS.
  • Spectra were generated on a Tecan Infinite M200 PRO using the following parameters:
    • Excitation: Recording at 638nm while exciting between 280nm and 610nm
    • Emission: Exciting at 509nm while recording between 535nm and 800nm
    • Absorbance: Measured between 300 and 800nm

Solubility & Handling

Storage instructions -20°C
Solubility overview Soluble in DMSO (100 mM)
Important This product is for RESEARCH USE ONLY and is not intended for therapeutic or diagnostic use. Not for human or veterinary use



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Chemical Data

Chemical name 3,6-Di-1-azetidinyl-9-(2,5-dicarboxyphenyl)xanthylium, inner salt trifluoroacetate
Molecular Weight 568.5
Chemical structure  Janelia Fluor® 549, free acid [2245946-45-4] Chemical Structure
Molecular Formula C27H22N2O5 · C2HF3O2
CAS Number 2245946-45-4
PubChem identifier 137919862
SMILES C1CN(C1)C2=CC3=C(C=C2)C(=C4C=CC(=[N+]5CCC5)C=C4O3)C6=C(C=CC(=C6)C(=O)[O-])C(=O)O.C(=O)(C(F)(F)F)O
Source Synthetic
Appearance Purple-grey solid
Licensing details

Sold under license from the Howard Hughes Medical Institute, Janelia Research Campus

References for Janelia Fluor® 549, free acid

References are publications that support the biological activity of the product
  • Synthesis of Janelia Fluor HaloTag and SNAP-Tag Ligands and Their Use in Cellular Imaging Experiments.

    Grimm JB et al (2017) Methods in molecular biology (Clifton, N.J.) 1663 : 179-188
  • A general method to improve fluorophores for live-cell and single-molecule microscopy.

    Grimm JB et al (2015) Nature methods 12 : 244-50, 3 p following 250

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