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Submit ReviewJanelia Fluor® 646, NHS ester
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)
Biological Activity for Janelia Fluor® 646, NHS ester
Key Information: Janelia Fluor® 646, NHS ester 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 NHS ester (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.
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.
HaloTag is a trademark of Promega Corporation, and SNAP-tag is a trademark of New England BioLabs, Inc.
Janelia Fluor is a registered trademark of Howard Hughes Medical Institute.
This product has been recently renamed. The previous name for this product was Janelia Fluor® 646, SE.
Scientific Data
Super-Resolution Microscopy
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Application of Janelia Fluor® 646, NHS ester in Cardiac Tissue. Super-resolution image (dSTORM) of muscle tissue from the left ventricle of an adult pig heart. Janelia Fluor 646, NHS ester 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, NHS ester
| Emission Color | Red |
|---|---|
| Brightness | |
| 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, NHS ester
| M. Wt | 593.71 |
| Formula | C33H31N3O6Si |
| Storage | Store at -20°C |
| Purity | ≥95% (HPLC) |
| CAS Number | 1811539-59-9 |
| PubChem ID | 124201858 |
| InChI Key | ODBCGJUBBYOJOS-UHFFFAOYSA-N |
| 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, NHS ester
| Solvent | Max Conc. mg/mL | Max Conc. mM | |
|---|---|---|---|
| Solubility | |||
| DMSO | 2.97 | 5 | |
| DMF | 29.69 | 50 |
Preparing Stock Solutions for Janelia Fluor® 646, NHS ester
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.
| 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, NHS ester
References for Janelia Fluor® 646, NHS ester
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, NHS ester, please let us know.
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5 Citations for Janelia Fluor® 646, NHS ester
Citations are publications that use Tocris products. Selected citations for Janelia Fluor® 646, NHS ester include:
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
Juan S et al (2021) SNX19 restricts endolysosome motility through contacts with the endoplasmic reticulum. Nat Commun 12 4552 PMID: 34315878
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, NHS ester from Tocris? Please let us know.
Reviews for Janelia Fluor® 646, NHS ester
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%
Protocols for Janelia Fluor® 646, NHS ester
The following protocol features additional information for the use of Janelia Fluor® 646, NHS ester (Cat. No. 6148).
Literature in this Area
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