Product overview

Name Janelia Fluor® 549, SE
Biological description

Cell permeable, yellow fluorescent dye supplied as an NHS ester / succinimidyl ester (SE) for coupling to primary amine (NHS) groups. NHS esters are used to label the primary amines of proteins and are commonly used for conjugating dyes to a protein or antibody.

May be used for cellular imaging when combined with the HaloTag or SNAP-tag self labelling systems. Suitable for confocal microscopy and super resolution microscopy (SRM) including techniques such as dSTORM (both live and fixed cells) and STED. 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, JF549-SE
Description

Yellow dye for coupling to NHS groups. Suitable for dSTORM, STED, confocal microscopy, live cell imaging and flow cytometry.

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Images

Fig 1. ß-tubulin expression in HeLa cells visualised using a Janelia Fluor® 549 conjugated secondary antibody.

Figure 1. β-tubulin expression in HeLa cells visualised using a Janelia Fluor® 549 conjugated secondary antibody. HeLa cells were stained using FITC Phalloidin (HB0814) and a mouse monoclonal β-tubulin (HB6491) antibody from Hello Bio which was visualised using a Janelia Fluor® 549 SE conjugated polyclonal goat anti-mouse antibody. For more details see protocols #1 and #2 in the application notes below.

Fig 2. GFAP expression in rat brain visualised using a Janelia Fluor® 549 conjugated secondary antibody.

Figure 2. GFAP expression in rat brain visualised using a Janelia Fluor® 549 conjugated secondary antibody. Rat horizontal brain sections were stained using mouse monoclonal GFAP (HB8267) and Neurofilament L (HB7266) antibodies from Hello Bio which were visualised using a Janelia Fluor® 549 SE conjugated goat anti-mouse antibody and a DyLight 488 conjugated goat anti- rabbit antibody. For more details see protocols #1 and #3 in the application notes below.

Fig 3. ß-tubulin expression in HeLa cells visualised using a Janelia Fluor® 549 conjugated secondary antibody.

Figure 3. β-tubulin expression in HeLa cells visualised using a Janelia Fluor® 549 conjugated secondary antibody. HeLa cells were stained using FITC Phalloidin (HB0814) and a mouse monoclonal β-tubulin antibody (HB6491) from Hello Bio which was visualised using a Janelia Fluor® 549 SE conjugated polyclonal goat anti- mouse antibody. For more details see protocols #1 and #2 in the application notes
Figure 4. Janelia Fluor® 549 conjugated secondary antibodies show superior antifade performance compared to those conjugated with DyLight 550

Optical Data

Fluorescence spectra Fluorescence Spectra
Reactivity Primary amines
Emission color Yellow
Max excitation wavelength 549 nm
Max emission wavelength 571 nm
Closest laser lines 532nm
Spectrally similar dyes Alexa Fluor® 546
Quantum Yield (φ) 0.88
Extinction Coefficient (ε) 101,000 M-1cm-1
Cell permeable Yes
Reactive Group NHS ester

Biological Data

Application notes

#Protocol 1: Conjugation of Janelia© Fluor 549 SE to antibodies

 

  • Using a desalting column, perform buffer exchange (following manufacturer instructions) of antibody into a carbonate buffer (100mM, pH 8-8.25)
  • Mix together the antibody and Janelia© Fluor 549 SE (prepared at 10mM in anhydrous DMSO or DMF) in a 15:1 molar ratio. Incubate in the dark for 60 minutes at room temperature with gentle mixing.
  • Add 10% by volume of 0.75M Tris-HCl pH7.4 (to a final concentration of 75mM) to stop the conjugation reaction. Incubate for 10-15 minutes at room temperature in the dark with gentle mixing.
  • Use a desalting column, perform buffer exchange (following manufacture instructions) of antibody into PBS 0.05% sodium azide. This step also removes any unbound dye

 

#Protocol 2: Immunocytochemistry

 

  • ICC was performed upon 4% PFA fixed HeLa cells using FITC Phalloidin (1:500) and a anti-β tubulin monoclonal antibody (HB6491, 1:2,000 / 0.5μg/ml). A polyclonal goat anti-mouse Janelia© Fluor 549 conjugated antibody was used at a dilution of 1:300 as a secondary antibody.
  • Please see our detailed immunocytochemistry protocol for details of the full protocol.

 

#Protocol 3: Immunohistochemistry

 

  • 40μm horizontal sections were cut from a 4% PFA fixed rat brain.
  • IHC(IF) was performed using mouse monoclonal anti-GFAP (HB8267, 1:1000 dilution / 1μg/ml) and rabbit monoclonal anti-NFL (HB7266, 1:2000 / 0.5μg/ml) antibodies. A polyclonal goat anti-mouse Janelia© Fluor 549 conjugated antibody was used at a dilution of 1:300 as a secondary antibody.
  • Please see our detailed immunohistochemistry protocol for details of the full protocol

Solubility & Handling

Storage instructions -20°C
Solubility overview Soluble in DMSO
Handling This compound is light and temperature sensitive; exposure to light may affect compound performance. We therefore recommend storing the material in a freezer and protecting from light.
Shipping conditions

Ship on ice

Important This product is for RESEARCH USE ONLY and is not intended for therapeutic or diagnostic use. Not for human or veterinary use

Calculators

Molarity

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Dilution

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Chemical Data

Chemical name 3,6-Di-1-azetidinyl-9-[2-carboxy-5-[[(2,5-dioxo-1-pyrrolidinyl)oxy]carbonyl]phenyl]xanthylium, inner salt
Molecular Weight 551.5
Chemical structure Janelia Fluor® 549, SE [1811539-32-8] Chemical Structure
Molecular Formula C31H25N3O7
CAS Number 1811539-32-8
PubChem identifier 124201856
SMILES C1CN(C1)C2=CC3=C(C=C2)C(=C4C=CC(=[N+]5CCC5)C=C4O3)C6=C(C=CC(=C6)C(=O)ON7C(=O)CCC7=O)C(=O)[O-]
Source Synthetic
InChiKey DWUIXAGWHCMXHN-UHFFFAOYSA-N
Licensing details

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

References for Janelia Fluor® 549, SE

References are publications that support the biological activity of the product
  • Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems.

    Binns TC et al (2020) Cell chemical biology 27 : 1063-1072.e7
  • A general method to fine-tune fluorophores for live-cell and in vivo imaging.

    Grimm JB et al (2017) Nature methods 14 : 987-994
  • 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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