Janelia Fluor® 635, SE

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Description: Red dye (Reactive group: NHS ester). Application: flow cytometry, confocal microscopy, super resolution microscopy. Suitable for live cell imaging
Alternative Names: JF 635,NHS
Chemical Name: 1-[10-[2-Carboxy-5-[[(2,5-dioxo-1-pyrrolidinyl)oxy]carbonyl]phenyl]-9,9-dimethyl-7-[1-(3-fluoroazetidinyl)]-9-silaanthracen-2(9H)-ylidene]-3-fluoroazetidinium, inner salt
Purity: ≥95% (HPLC)
Protocols (1)
Literature (1)

Biological Activity for Janelia Fluor® 635, SE

Key Information: Janelia Fluor® 635, SE is a red fluorogenic 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) techniques including dSTORM (in both live and fixed cells). 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 635 nm and 652 nm, respectively; quantum yield = 0.56; extinction coefficient = 167,000 M-1cm-1 (measured in ethanol or TFE plus 0.1% TFA); A280 correction factor = 0.0524; lactone-zwitterion equilibrium constant (KL-Z) <0.0001. Exhibits low nonspecific background staining.

Please see the protocol for further information on protein/antibody labeling and conjugation.

To measure the absorbance spectrum of this dye we recommend the following solvent: ethanol or trifluoroethanol plus 0.1% TFA.

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

Confocal Microscopy Applications on Mitochondria for Janelia Fluor® 635, SE View Larger

Applications on mitochondria for Janelia Fluor® 635, SE. Application of Janelia Fluor® 635, SE dye on mitochondria; Left: Mitochondria were labeled with anti-TOM20 primary antibodies. The secondary antibodies were conjugated to JF 635 dye. Maximum intensity projection of confocal z-stack, recorded on an Olympus FV1200 confocal microscope. Right: Enlarged portion of left-hand image. Images kindly provided by Dr Kirstin Elgass, Monash University.

Licensing Information

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

Optical Data for Janelia Fluor® 635, SE

Janelia Fluor<sup>®</sup> 635, SE Dye Spectra
Emission Color Red
λabs 635 nm
λem 652 nm
Extinction Coefficient (ε) 167,000 M-1cm-1
Quantum Yield (φ) 0.56
Closest Laser line 635 nm
Reactive Group NHS ester
Reactivity Primary amines
Cell Permeable Yes
Correction Factor 280 0.0524
Application Confocal Microscopy, Super Resolution Microscopy, Flow Cytometry
Alternative For Alexa Fluor® 633, Atto 633, CF633

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® 635, SE

M. Wt 629.69
Formula C33H29F2N3O6Si
Storage Store at -20°C
Purity ≥95% (HPLC)
PubChem ID 132470914
Smiles O=C(ON1C(CCC1=O)=O)C2=CC=C(C([O-])=O)C(C(C3=CC=C(N4CC(F)C4)C=C3[Si]5(C)C)=C(C=C/6)C5=CC6=[N+]7CC(F)C\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® 635, SE

Solvent Max Conc. mg/mL Max Conc. mM
DMSO 62.97 100

Preparing Stock Solutions for Janelia Fluor® 635, SE

The following data is based on the product molecular weight 629.69. 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 1.59 mL 7.94 mL 15.88 mL
5 mM 0.32 mL 1.59 mL 3.18 mL
10 mM 0.16 mL 0.79 mL 1.59 mL
50 mM 0.03 mL 0.16 mL 0.32 mL

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Product Datasheets for Janelia Fluor® 635, SE

Certificate of Analysis / Product Datasheet
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References for Janelia Fluor® 635, SE

References are publications that support the biological activity of the product.

Grimm et al (2017) A general method to fine-tune fluorophores for live-cell and in vivo imaging. Nat.Methods 14 987 PMID: 28869757

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® 635, SE, please let us know.

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Citations for Janelia Fluor® 635, SE

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Protocols for Janelia Fluor® 635, SE

The following protocol features additional information for the use of Janelia Fluor® 635, SE (Cat. No. 6419).

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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  • Fluorescent Probes for Imaging Bacteria
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