SYTO 9 Stain

SYTO 9 stain is an excellent green-fluorescent nuclear and chromosome counterstain that is permeant to both prokaryotic and eukaryotic cell membranes. SYTO 9 stain has a high affinity for DNA and exhibits enhanced fluorescence upon binding with an excitation maximum at 483 nm and fluorescence emission maximum at 503 nm.

SYTO 9 stain is particularly useful as a nuclear counterstain for bacterial assays since it stains both live and dead Gram-positive and Gram-negative bacteria.

SYTO 9 stain dashboard

Initial brightness

Live-cell SYTO dyes are permeant to both eukaryotic and prokaryotic membranes, and exhibit enhanced fluorescence upon binding to both DNA and RNA.  

Photostability in buffer


Photostability in antifade


SYTO 9 stain products

The SYTO green-fluorescent nucleic acid stains have proven valuable in a broad range of research applications. SYTO 9 stain is particularly used for staining live and dead Gram-positive and Gram-negative bacteria.

SYTO® 9 stain

Live/dead analysis of Streptomyces antibioticus ETH7451 cultures.

The mycelium was stained with SYTO 9 dye and propidium iodide (components of the LIVE/DEAD BacLight Bacterial Viability Kit, Cat. Nos. L7007, L7012, L13152). Live portions fluoresce green, and membrane-compromised portions fluoresce red. Image contributed by Jesus Sanchez and Marisol Fernandez, Microbiology Area, University of Oviedo, Spain, and reproduced with the permission of Microbiology 148, 405 (2002)


High-performance nucleic acid stains

Unlike our range of nuclear counterstains, SYTO dyes do not act exclusively as nuclear stains in live cells and should not be equated with DNA-selective compounds (such as DAPI) which stain nuclei in live animal cells. Eukaryotic cells incubated with SYTO dyes generally show cytoplasmic or mitochondrial staining, as well as nuclear staining.

Nuclear counterstains provide highly selective nuclear staining with little or no cytoplasmic labeling and a choice of colors for multiplexing with other labels. Additionally, some of the stains can also be used in cell cycle analyses using high-content imaging and flow cytometry.

TO-PRO-3 iodide stained cell

A fixed, permeabilized, and labeled muntjac skin fibroblast. Mitochondria were labeled with mouse anti–OxPhos Complex V inhibitor protein antibody and visualized using orange-fluorescent Alexa Fluor 555 goat anti–mouse IgGantibody. F-actin was labeled with green-fluorescent Alexa Fluor 488 phalloidin, and the nucleus was stained with TO-PRO-3 iodide (pseudocolored magenta).



Molecular Probes Handbook

Cell stain tool

The significantly revised 11th Edition is the most complete fluorescence labeling and detection reference available. The Molecular Probes Handbook can help you achieve the best experimental results for your fluorescence labeling and detection experiments. View the handbook online or order your own copy.

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Order your copy of the Handbook

Antifade reagents

Cell stain tool

Antifade reagents suppress photobleaching and preserve the signals of your fluorescently labeled target molecules. They offer excellent compatibility with a multitude of dyes across the spectrum, making them especially valuable tools for multicolor applications. For added convenience, some formulations include the nuclear counterstain DAPI, eliminating the need for a separate counterstaining step.

Learn more about SlowFade Antifade reagents
Learn more about ProLong Antifade reagents

Cell stain tool

Cell stain tool

Stain your own cell by using our simulation tool to develop reproducible results with many of our signature fluorescent dyes. Develop your multiplexing strategy for antibody probes, reactive dyes, and counterstains to create your perfectly labeled fluorescent cell.

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Fluorescence SpectraViewer


Plot and compare spectra and check the spectral compatibility for common fluorophores including all of the fluorescent probes from Thermo Fisher Scientific. The Fluorescence SpectraViewer tool is formatted for both microscope imaging and flow cytometry applications.

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Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.