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Submit ReviewHoechst Janelia Fluor® 646
Description: Fluorogenic, red-emitting DNA probe. Used for: fixed and live-cell imaging. Application: confocal microscopy, super resolution microscopy (SRM) (PALM, PAINT), lattice light sheet microscopy
Alternative Names: Hoechst JF 646,JF646-Hoechst
Chemical Name: 2-(3-(Azetidin-1-ium-1-ylidene)-7-(azetidin-1-yl)-5,5-dimethyl-3,5-dihydrodibenzo[b,e]silin-10-yl)-4-((2-(2-(2-(4-(4-(5-(4-methylpiperazin-1-yl)-1H,3'H-[2,5'-bibenzo[d]imidazol]-2'-yl)phenoxy)butanamido)ethoxy)ethoxy)ethyl)carbamoyl)benzoate
Purity: ≥85% (HPLC)
Biological Activity for Hoechst Janelia Fluor® 646
Key information: Hoechst Janelia Fluor® 646 is a fluorogenic red-emitting DNA probe. Suitable for fixed and live-cell imaging.
Application:confocal microscopy, super resolution microscopy (SRM) (including PALM and PAINT), lattice light sheet microscopy.
Properties and Photophysical Data: Hoechst Janelia Fluor® 646 preferentially stains and binds minor groove of AT-rich regions. The compound can be combined with fluorogenic green-emitting DNA probe Hoechst Janelia Fluor® 526 (Cat. No. 7313) for multiplexing experiments. Hoechst Janelia Fluor® 646 can also be combined with Hoechst Janelia Fluor® 526 to perform dual-color STED using the same depletion laser (λdep = 775 nm). Sub-diffraction spatial resolution STED imaging can be achieved using Hoechst Janelia Fluor® 646 in E. coli cells (~100 nM - 1 μM). Hoechst Janelia Fluor® 646 is a desirable alternative to large oligonucleotide-conjugated antibodies for PAINT experiments, particularly for bacterial studies. Excitation and emission maxima (λ) are 655 nm and 670 nm, respectively; quantum yield = 0.54; extinction coefficient = 152,000 M-1cm-1.
Hoechst Janelia Fluor® 646 is fluorogenic and fluoresces only once bound to DNA, enabling hassle-free no-wash experiments.
To measure the absorbance spectrum of Hoechst Janelia Fluo® 646 we recommend the following solvent: TFE plus 0.1% TFA.
Scientific Data
Confocal Microscopy
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Application of Hoechst Janelia Fluor® 646 in U2OS cells. Fixed U2OS cells were stained with Hoechst Janelia Fluor® 646 (1 µM) for 1 hour and imaged without an intermediate washing step on a LSM980 confocal microscope (Zeiss) using the following configuration: excitation: 633 nm / emission: 638–759 nm. Image kindly provided by Prof. Luke Lavis, Howard Hughes Medical Institute, Janelia Research Campus.
Licensing Information
Sold under license from the Howard Hughes Medical Institute, Janelia Research Campus
Optical Data for Hoechst Janelia Fluor® 646
| Emission Color | Red |
|---|---|
| Brightness | |
| λabs | 655 nm |
| λem | 670 nm |
| Extinction Coefficient (ε) | 152,000 M-1cm-1 |
| Quantum Yield (φ) | 0.54 |
| Closest Laser line | 640 nm |
| Cell Permeable | Yes |
| Application | Super Resolution Microscopy (PALM, PAINT), Confocal Microscopy, Lattice Light Sheet Microscopy |
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 Hoechst Janelia Fluor® 646
| M. Wt | 1119.39 |
| Formula | C64H70N10O7Si |
| Storage | Store at -20°C |
| Purity | ≥85% (HPLC) |
| CAS Number | 2462011-60-3 |
| InChI Key | DTAPBNBSCGEQMS-UHFFFAOYSA-N |
| Smiles | C[Si]1(C)C2=C/C(C=CC2=C(C3=CC(C(NCCOCCOCCNC(CCCOC4=CC=C(C5=NC6=C(C=C(C=C6)C7=NC8=C(C=CC(N9CCN(C)CC9)=C8)N7)N5)C=C4)=O)=O)=CC=C3C([O-])=O)C%10=CC=C(N%11CCC%11)C=C%101)=[N+]%12CCC/%12 |
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 Hoechst Janelia Fluor® 646
| Solvent | Max Conc. mg/mL | Max Conc. mM | |
|---|---|---|---|
| Solubility | |||
| DMSO | 11.19 | 10 |
Preparing Stock Solutions for Hoechst Janelia Fluor® 646
The following data is based on the product molecular weight 1119.39. 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 |
|---|---|---|---|
| 0.1 mM | 8.93 mL | 44.67 mL | 89.33 mL |
| 0.5 mM | 1.79 mL | 8.93 mL | 17.87 mL |
| 1 mM | 0.89 mL | 4.47 mL | 8.93 mL |
| 5 mM | 0.18 mL | 0.89 mL | 1.79 mL |
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Product Datasheets for Hoechst Janelia Fluor® 646
References for Hoechst Janelia Fluor® 646
References are publications that support the biological activity of the product.
Legant et al (2016) High density three-dimensional localization microscopy across large volumes. Nat.Methods 13 359 PMID: 26950745
Grimm et al (2017) A general method to fine-tune fluorophores for live-cell and in vivo imaging. Nat.Methods 14 987 PMID: 28869757
Saphn et al Bleaching-independent, whole-cell, 3D and multi-color STED imaging with exchangeable fluorophores. BioRxiv - Paper not yet peer reviewed
Spahn et al (2019) Whole-Cell, 3D, and multicolor STED imaging with exchangeable fluorophores. Nano Lett. 19 500 PMID: 30525682
Spahn et al (2018) A toolbox for multiplexed super-resolution imaging of the E. coli nucleoid and membrane using novel PAINT labels. Sci. Rep. 8 14768 PMID: 30282984
If you know of a relevant reference for Hoechst Janelia Fluor® 646, please let us know.
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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
- Aptamer-based RNA Imaging Reagents
- Fluorescent Probes for Imaging Bacteria
- TSA VividTM Fluorophore Kits
- TSA Reagents for Enhancing IHC, ICC & FISH Signals