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SYTO™ 9 Green Fluorescent Nucleic Acid Stain, 100 μL - FAQs

View additional product information for SYTO™ Green Fluorescent Nucleic Acid Stains - FAQs (S32703, S7575, S7574, S7573, S7572, S7578, S7556, S34854, S7576, S34855, S7559)

4 product FAQs found

How do SYTO dyes bind to DNA?

The binding mode of SYTO nucleic acid stains is unknown. However, the behavior of these and related nucleic acid dyes suggests the following binding properties:

1.They appear to contact the solvent (suggested by sensitivity to salt, divalent cations, and in particular, SDS) and thus are likely to have contacts in the grooves.
2.All SYTO dyes appear to show some base selectivity and are thus likely to have minor groove contacts.
3.They can be removed from nucleic acid via ethanol precipitation; this characteristic is not shared by ethidium bromide and other intercalators. Likewise, the dyes are not removed from nucleic acid via butanol or chloroform extraction. These extraction methods do remove ethidium bromide from nucleic acid. 4. SYTO binding is not affected by nonionic detergents.
5. SYTO dyes are not quenched by BrdU, so they do not bind nucleic acids in precisely the same way as Hoechst 33342 and DAPI ((4′,6-diamidino-2-phenylindole).

SYBR Green I has shown little mutagenicity on frameshift indicator strains, indicating that it isn't likely to strongly intercalate.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

What are the best nucleic acid stains for labeling nuclei in live cells in green and red?

SYTO 9 dye is one good choice for green; it is similar to fluorescein in excitation and emission wavelength. SYTO 59 dye is a good choice for red; it is similar to Texas Red. Both dyes are cell-permeant and stain DNA well, resulting in good nuclear labeling in live cells. With too high a concentration of dye and/or too long an incubation time, both may also label RNA, resulting in cytoplasmic and nucleolar staining, particularly with SYTO 59 dye.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

I have a LIVE/DEAD BacLight Bacterial Viability kit that has SYTO 9 and propidium iodide in it. Will I be able to stain eukaryotic cells that have engulfed bacteria and determine if the bacteria are alive or dead using this kit?

Unfortunately, no. SYTO 9 will label the nuclei of live or dead cells, including the eukaryotic cells. Propidium iodide is cell impermeant, and will only enter dead cells. If the eukaryotic cells are dead, they will label with propidium iodide as well. If the eukaryotic cells are alive, propidium iodide will not be able to enter and thus will not label the bacteria inside, whether the bacteria are alive or dead. We are not aware of any way to do a viability assay of bacteria once they have been engulfed by cells.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

I am having a hard time separating my bacteria from instrument noise. How can I optimize my signal?

Electronic noise is due to stray light collected by the system optics and/or low-level electronic signals. Noise may be eliminated or reduced through correct setup of instrument threshold and photomultiplier tube (PMT) voltage. The easiest way to differentiate a bacterial population from other small particles and electronic noise is to label the bacteria with a fluorescent stain and use the fluorescence emission to identify the population of interest. SYTO 9 is a great stain to label all cells and is detected in the FITC channel.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.