Hoechst Janelia Fluor® 646

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Description: Fluorogenic, red-emitting DNA probe
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: ≥90% (HPLC)
Literature (1)

Biological Activity for Hoechst Janelia Fluor® 646

Hoechst Janelia Fluor® 646 is a fluorogenic red-emitting DNA probe; it 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 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. Hoechst Janelia Fluor® 646 exhibits a quantum yield (QY) of 0.54; extinction coefficicent 152, 000; excitation maximum = 655 nm; emission maximum = 670 nm.

Fluorogenic: fluoresces only once bound to DNA, enabling hassle-free no-wash experiments. Hoechst Janelia Fluor® 646 is suitable for multicolor microscopy experiments and for use in live cell imaging.

To measure the absorbance spectrum of Hoechst Janelia Fluo® 646 we recommend the following solvent: TFE plus 0.1% TFA.

Licensing Information

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

Optical Data for Hoechst Janelia Fluor® 646

Hoechst Janelia Fluor<sup>®</sup> 646 Dye Spectra
Emission Color Red
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

Technical Data for Hoechst Janelia Fluor® 646

M. Wt 1119.39
Formula C64H70N10O7Si
Storage Store at -20°C
Purity ≥90% (HPLC)
CAS Number 2462011-60-3
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
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.

Select a batch to recalculate based on the batch molecular weight:
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

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:

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