Janelia Fluor® 646, SE

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Description: Red 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 646,NHS
Chemical Name: 1-[7-(1-Azetidinyl)-10-[2-carboxy-5-[[(2,5-dioxo-1-pyrrolidinyl)oxy]carbonyl]phenyl]-9,9-dimethyl-9-silaanthracen-2(9H)-ylidene]azetidinium, inner salt
Purity: ≥95% (HPLC)
Citations (5)
Reviews (1)
Protocols (1)
Literature (1)

Biological Activity for Janelia Fluor® 646, SE

Key Information: Janelia Fluor® 646, 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) and STED. 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®. Can be multiplexed for two color imaging with Janelia Fluor® 549 SE (Cat. No. 6147). Excitation and emission maxima (λ) are 646 nm and 664 nm, respectively; quantum yield = 0.54; extinction coefficient = 152,000 M-1cm-1 (measured in TFE plus 0.1% TFA); A280 correction factor = 0.19; lactone-zwitterion equilibrium constant (KL-Z) = 0.0012.

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

We recommend that stock solutions of this dye are prepared in anhydrous DMF.

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

Super-Resolution Microscopy Application of Janelia Fluor® 646, SE in Cardiac Tissue. View Larger

Application of Janelia Fluor® 646, SE in Cardiac Tissue. Super-resolution image (dSTORM) of muscle tissue from the left ventricle of an adult pig heart. Janelia Fluor 646, SE was used to label collagen VI, which is present on the cell plasma membrane, and imaged with a 642 nm excitation laser. A clearer structure is achieved in comparison with the widefield image (top right). Scale: 2 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® 646, SE

Janelia Fluor<sup>®</sup> 646, SE Dye Spectra
Emission Color Red
λabs 646 nm
λem 664 nm
Extinction Coefficient (ε) 152,000 M-1cm-1
Quantum Yield (φ) 0.54
Closest Laser line 640 nm
Reactive Group NHS ester
Reactivity Primary amines
Cell Permeable Yes
Correction Factor 280 0.19
Application Confocal Microscopy, dSTORM, STED, Flow Cytometry
Alternative For Alexa Fluor® 647, Atto 647, Atto 647N, CF640R, CF647, Cyanine 5

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.

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Technical Data for Janelia Fluor® 646, SE

M. Wt 593.71
Formula C33H31N3O6Si
Storage Store at -20°C
Purity ≥95% (HPLC)
CAS Number 1811539-59-9
PubChem ID 124201858
Smiles O=C(ON1C(CCC1=O)=O)C2=CC=C(C([O-])=O)C(C(C3=CC=C(N4CCC4)C=C3[Si]5(C)C)=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® 646, SE

Solvent Max Conc. mg/mL Max Conc. mM
DMSO 2.97 5
DMF 29.69 50

Preparing Stock Solutions for Janelia Fluor® 646, SE

The following data is based on the product molecular weight 593.71. 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
0.5 mM 3.37 mL 16.84 mL 33.69 mL
2.5 mM 0.67 mL 3.37 mL 6.74 mL
5 mM 0.34 mL 1.68 mL 3.37 mL
25 mM 0.07 mL 0.34 mL 0.67 mL

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Product Datasheets for Janelia Fluor® 646, SE

Certificate of Analysis / Product Datasheet
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References for Janelia Fluor® 646, SE

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

Schmidt et al (2016) Live cell imaging reveals the dynamics of telomerase recruitment to telomeres. Cell 166 1188 PMID: 27523609

Li et al (2016) Real-time imaging of Huntingtin aggregates diverting target search and gene transcription. Elife 5 e17056 PMID: 27484239

Legant et al (2016) High-density three-dimensional localization microscopy across large volumes. Nat.Methods 13 359 PMID: 26950745

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

Ticau et al (2015) Single-molecule studies of origin licensing reveal mechanisms ensuring bidirectional helicase loading. Cell 161 513 PMID: 25892223

Hong et al (2009) Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome. Proc.Natl.Acad.Sci.U.S.A. 106 14276 PMID: 19666497

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® 646, SE, please let us know.

Keywords: Janelia Fluor 646, SE, Janelia Fluor 646, SE supplier, JF646, Janelia, Fluor, 646-SE, fluorescent, dyes, NHS, ester, self-labeling, tag, systems, microscopy, cell, permeable, super, resolution, STED, flow, cytometry, JF, 646,, Amine, Reactive, Dyes, Flow, Cytometry, 6148, Tocris Bioscience

5 Citations for Janelia Fluor® 646, SE

Citations are publications that use Tocris products. Selected citations for Janelia Fluor® 646, SE include:

Juan S et al (2021) SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum. Nat Commun 12 4552 PMID: 34315878

Diane S et al (2020) High-speed single molecule imaging datasets of membrane proteins in rat basophilic leukemia cells. Data Brief 30 105424 PMID: 32322610

Rachel et al (2020) Molecular mechanism for direct actin force-sensing by α-catenin. Elife 9 PMID: 32969337

Nina et al (2022) Nanoscale segregation of channel and barrier claudins enables paracellular ion flux. Nat Commun 13 4985 PMID: 36008380

Bridget S et al (2022) Docking of Syk to FcεRI is enhanced by Lyn but limited in duration by SHIP1. Mol Biol Cell 33 ar89 PMID: 35793126

Do you know of a great paper that uses Janelia Fluor® 646, SE from Tocris? Please let us know.

Reviews for Janelia Fluor® 646, SE

Average Rating: 4 (Based on 1 Review.)

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JF646 labeled proteins in vitro.
By Saumya Saurabh on 02/26/2018
Assay Type: In Vitro
Species: Other

I used this dye for labeling bacterial proteins in vitro. The labeling method is pretty straight-forward as for any NHS-protein coupling. The dye is highly photostable as determined by single protein tracking on lipid bilayers (image of single proteins attached, scale bar is 5 micron). The only reason I give the product 4 stars instead of 5 is the packaging. The dye is shipped as a solid in a glass bottle with a flexible rubber cap. Most of the dye gets stuck inside and on the surface of this cap; thus not delivering a full value for money. I will highly recommend the manufacturers to use bottles with plastic caps so that the dye can be recovered a 100%

review image

Protocols for Janelia Fluor® 646, SE

The following protocol features additional information for the use of Janelia Fluor® 646, SE (Cat. No. 6148).

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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