Invitrogen™ SYBR™ Safe DNA Gel Stain in 0.5X TBE

Catalog No.	Quantity
S33101	4 L
S33100	1 L

Catalog No. S33101 Supplier Invitrogen™ Supplier No. S33101

Description

Developed specifically for reduced mutagenicity – to be safer than ethidium bromide for staining DNA in agarose or acrylamide gels

SYBR Safe stain is less mutagenic than ethidium bromide and offers better sensitivity than ethidium bromide. Supplied as a premixed solution that can be used like an ethidium bromide solution, either in the gel during the electrophoresis run or as a post-run stain. Bound to nucleic acids, the green-fluorescent SYBR Safe stain has fluorescence excitation maxima at ∽280 and ∽502nm, and an emission maximum at ∽530nm. SYBR Safe DNA gel stain is also available as 4L (S-33101) of ready-to-use solution. The SYBR Safe DNA Gel Stain Starter Kit (S-33110, sold separately) includes 1L of SYBR Safe DNA gel stain and one photographic filter (S-37100).

Agarose Gel Electrophoresis, DNA and RNA Purification and Analysis, Nucleic Acid Gel Electrophoresis and Blotting

Order Info

Shipping Condition: Room temperature

Specifications

• Content And Storage: • Supplied as a ready-to-use solution in 0.5X TBE
  
  Store at room temperature in the original container.
  
• Detection Location: In-Gel Detection
• Detection Method: Fluorescence
• Label or Dye: SYBR Safe
• Quantity: 4 L
• Shipping Condition: Room Temperature
• Target Molecule: DNA
• Product Type: DNA Gel Stain

Frequently Asked Questions (FAQs)

Why do I sometimes see speckles in my gel when using SYBR Safe DNA Gel Stain?

Many whitening agents used in clothing, as well as some fungi and bacteria, fluoresce at the same wavelengths as SYBR Safe DNA gel stain. These contaminants within or on the surface of the gel may produce this speckling.

What is the pH range of SYBR dyes?

The SYBR dyes are useful only over a narrow range of pH, from about 7 to 8. Outside this range, the fluorescent signal diminishes rapidly.

Which direction does the SYBR Safe dye run during electrophoresis?

Similarly to ethidium bromide, SYBR Safe DNA Gel Stain runs in the opposite direction of the migrating DNA. This has no practical effect on the use of gels cast with SYBR Safe DNA Gel Stain, as only the very bottom of the gel will have a lower concentration of stain. This effect can be partially counteracted by staining the gel with SYBR Safe DNA Gel Stain after electrophoresis. Solutions of dye should not be added to the running buffer as this can cause breakdown of the dye at the electrodes and release toxic volatile compounds into the air.

Does ethanol precipitation remove the SYBR Safe dye?

SYBR Safe DNA Gel Stain is easily removed from nucleic acids by ethanol precipitation.

Can I reuse SYBR Safe DNA Gel Stain for a second gel?

We strongly discourage the reuse of SYBR Safe DNA Gel Stain, as this practice significantly lowers sensitivity.

Is SYBR Safe DNA Gel Stain compatible with the same applications as ethidium bromide?

Yes. SYBR Safe DNA Gel Stain is compatible with all downstream applications we have tested so far, including excising PCR products from gels, gel purification, Gateway cloning, TOPO cloning, and restriction enzyme cloning. If you have a unique application that works with SYBR Safe DNA Gel Stain, send us the details at techsupport@thermofisher.com.

What other excitation wavelengths can I use to visualize SYBR Safe DNA Gel Stain?

SYBR Safe DNA Gel Stain has two main excitation peaks: in the UV region at 280 nm, and in the visible region at 502 nm. Thus, wavelengths from 254 nm to 300 nm UV excitation will work, as will excitation with 488 nm lasers, 470 nm LEDs, and broad blue light sources (such as the Safe Imager Blue-Light Transilluminator (Cat. No. S37102). Maximal excitation occurs at 502 nm; the Safe Imager Blue-Light Transilluminator is therefore the best choice for excitation of SYBR Safe DNA Gel Stain. You can find the full excitation and emission spectra for SYBR Safe DNA Gel Stain online and also in the protocol provided with the stain.

Can I view SYBR Safe DNA gel stain with my ethidium bromide filter and camera settings?

Some ethidium bromide filters allow the transmission of all light above 500 nm. These filters (which are often yellow) and their associated camera settings can be used with SYBR Safe DNA Gel Stain, usually with only minor adjustments to the exposure or gain. Other ethidium bromide filters (often red) only transmit light around or above 600 nm; these filters and their associated camera settings are not suitable for use with SYBR Safe DNA Gel Stain.

What is the recommended filter for my gel documentation system?

Please go here (https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/nucleic-acid-gel-electrophoresis/dna-stains/sybr-safe.html) and click on the “Filter Recommendations” tab to see filter recommendations for use with SYBR Safe DNA Gel Stain. Note that the excitation and emission spectra of SYBR Safe DNA Gel Stain are very similar to those of SYBR Green I, SYBR Green II, and SYBR Gold dyes, as well as fluorescein (FITC). Therefore, filters appropriate for these dyes can also be used. A camera filter is not required with the Safe Imager Blue-Light Transilluminator; the amber filter provided with the instrument serves this purpose.

Can bands be seen on a UV transilluminator without the use of emission filters?

Bands stained with SYBR Safe DNA Gel Stain are visible to the eye on a 300 nm transilluminator. If a camera is not equipped with a filter, the excitation light will be captured on the image to give a 'washed out' appearance. You can obtain optimum detection by photographing the gel using a UV-compatible emission filter with your CCD or film camera. UV bulbs may also emit some infrared (IR); if your camera lens is not specially coated to block IR, an IR-blocking filter is needed to prevent the appearance of faint images of the UV bulbs behind your gel. For optimum detection and complete safety, use the Safe Imager Blue-Light Transilluminator.

What are the advantages of using blue light to view DNA stained with SYBR Safe DNA Gel Stain?

Unlike UV light, blue light causes minimal damage to DNA. Use of SYBR Safe DNA Gel Stain and the Safe Imager Blue-Light Transilluminator gives improved cloning efficiency over DNA stained with ethidium bromide and exposed to UV light.

Can I use the ethidium bromide filters on my camera to image SYBR dyes?

This is not recommended. Most deep amber/orange ethidium bromide filters have a cutoff value around 550 nm. The SYBR Green dyes emit at 520 nm, which will not be detected using this filter.

How do I view DNA stained with SYBR Safe DNA Gel Stain?

DNA stained with SYBR Safe DNA Gel Stain can be viewed using a blue-light transilluminator such as our Safe Imager 2.0 Blue-Light Transilluminator or a standard UV transilluminator. If you plan to use the DNA for cloning, avoid exposing DNA stained with SYBR Safe DNA Gel Stain to UV light.

How many parts per million (ppm) of SYBR Safe DNA Gel Stain are there in a 1X solution of the stain?

The SYBR Safe DNA Gel Stain content in a 1X solution is less than 1 ppm.

Can agarose gels be cast with SYBR Safe DNA Gel Stain in them?

Yes. Simply substitute a SYBR Safe DNA Gel Stain solution for the buffer when preparing the molten agarose. If you are using the 10,000X SYBR Safe DNA Gel Stain concentrate, dilute the concentrated stain 1:10,000 in agarose gel buffer (e.g., 1X TBE or 1X TAE) and add the buffer/stain solution to the powdered agarose. You can heat the agarose/SYBR Safe DNA Gel Stain mixture briefly in the microwave.

Is SYBR Safe DNA Gel Stain the same as SYBR Green I dye?

All SYBR dyes have similar spectral properties, but have different chemical compositions. All SYBR dyes bind to dsDNA, ssDNA and RNA but vary in sensitivity. SYBR Safe DNA Gel Stain was specifically developed as a safer alternative to ethidium bromide. SYBR Green I is an ultrasensitive stain for dsDNA, and SYBR Green II is a highly sensitive stain for RNA and ssDNA. All SYBR dyes are optimally excited by the Safe Imager Blue-Light Transilluminator.

What is the difference between your SYBR Safe Stain and ethidium bromide?

SYBR Safe Stain is non-mutagenic and non-toxic. It shows very similar sensitivity in the UV range, ~500 pg/band, with equivalent resolution to ethidium bromide. For imaging, ethidium bromide is visualized using a standard UV transilluminator, while SYBR Safe stain can be viewed with either UV (~280 nm), laser scanners with visible light capability, or blue light (450 to 500 nm).

How should I dispose of SYBR DNA Gel Stain?

Disposal regulations vary. Please contact your safety office or local municipality for disposal guidelines.

What are the differences between all the SYBR dyes?

Different SYBR dyes bind to dsDNA, ssDNA, and RNA, but vary in the sensitivity and specificity with which they bind to different nucleic acids. SYBR Green I Nucleic Acid Gel Stain is used for staining dsDNA and ssDNA. SYBR Green II RNA Gel Stain will stain dsDNA and ssDNA but has better sensitivity for RNA. SYBR Gold Acid Gel Stain was developed after SYBR Green I and II and is the most sensitive fluorescent gel stain offering the highest sensitivity for both DNA and RNA. SYBR Safe DNA Gel Stain is a reduced mutagenicity formula designed for use with blue light systems. It is less sensitive than the SYBR Green I and II but comparable to ethidium bromide.

Please check the following link for additional details regarding the different SYBR dyes: The Molecular Probes Handbook: Nucleic Acid Detection on Gels, Blots and Arrays

Will ethanol precipitation remove the SYBR Safe dye from my DNA?

Yes, SYBR Safe stain is easily removed from nucleic acids by ethanol precipitation or by the ethanol wash steps used for purification spin columns.

Is SYBR Safe stain available in any precast gels?

Several E-Gel products are available with SYBR Safe DNA gel stain. These gels can be used in the same manner as their ethidium bromide counterparts, with the additional safety and application benefits of SYBR Safe. To learn more about these products, search "E-Gel Precast Agarose Gels" from the Thermo Fisher Scientific website home page.

Does use of SYBR Safe stain affect cloning efficiencies after gel purification?

We have found a distinct advantage to using SYBR Safe stain rather than ethidium bromide when purifying DNA from gels for downstream use. SYBR Safe stain is compatible with blue light imaging systems as well as UV. Using blue light to visualize the DNA allows you to purify a band with virtually no UV-induced nicking or crosslinking. This can dramatically increase cloning efficiency. Data from one such experiment showing higher cloning efficiency with PCR products visualized with SYBR Safe and blue light vs. ethidium bromide and UV light can be seen on the information page for Safe Imager 2.0 Blue-Light Transilluminator (Cat. No. G6600) and on the SYBR Safe home page.

Does SYBR Safe stain need to be used in a dark room?

We recommend that SYBR Safe stain be protected from light during storage and gel staining. However, it is sufficiently stable to withstand UV illumination for >30 minutes; realistically, hours of constant UV or bright room light exposure are required to cause any significant loss of signal.

Is SYBR Safe stain microwaveable?

SYBR Safe stain may be briefly microwaved with no loss of performance. However, we do not know the effect of repeated or very long duration microwaving.

Can I reuse SYBR Safe stain for a second gel?

We strongly discourage the reuse of SYBR Safe stain, as this practice significantly lowers sensitivity.

What is the lower limit of detection of SYBR Safe stain?

SYBR Safe stain yields the same sensitivity as ethidium bromide - roughly 500 pg/band in a minigel for fragments larger than 200 bp viewed on a 300 nm transilluminator.

How much of the 10,000X SYBR Safe concentrate should I use for one gel?

Dilute SYBR Safe stain concentrate 10,000-fold in TAE or TBE buffer prior to use. 50 mL of 1X stain is sufficient for most minigels (e.g., dilute 5 µL of concentrate into 50 mL buffer for a 1X solution). For larger gels, increase volumes proportionally, ensuring that the entire gel is fully immersed during staining.

Is SYBR Safe stain compatible with the same applications as ethidium bromide?

SYBR Safe DNA gel stain is compatible with all downstream applications we have tested so far, including excising PCR products from gels, gel purification, Gateway cloning, TOPO cloning, and restriction enzyme cloning. The use of SYBR Safe DNA gel stain with non-UV blue light emitted by the Safe Imager instrument allows you to purify DNA with virtually no UV-induced nicking or crosslinking compared to ethidium bromide and UV, resulting in dramatically increased cloning efficiencies. If you have a unique application that works with SYBR Safe DNA gel stain, send us the details at techsupport@thermofisher.com.

Why do I sometimes see "speckles" in my gel when using SYBR Safe stain?

Many whitening agents used in clothing, some synthetic fibers, as well as some fungi and bacteria, fluoresce at the same wavelength as SYBR Safe stain. These contaminants within or on the surface of the gel may produce this “speckling”. This can be avoided by being careful with preparation of the gel (i.e. try to keep the gel dust free). Alternatively, to obtain a publication quality image you may be able to preferentially photobleach some contaminants by leaving the gel on the UV box for 15-30 minutes, where the speckles will disappear before the SYBR stain photobleaches.

What are the optimal excitation wavelengths for visualizing SYBR Safe stain?

SYBR Safe DNA gel stain has two main excitation peaks: in the UV region at 280 nm, and in the visible region at 502 nm. Thus, 254 nm or 300 nm UV excitation will work, as will 488 nm lasers, 470 nm LEDs, and broad blue excitation (such as the Safe Imager 2.0 Blue-Light Transilluminator, Cat. No. G6600). Maximal excitation occurs at 502 nm; the Safe Imager 2.0 Blue-Light Transilluminator is therefore the best choice for excitation of SYBR Safe DNA gel stain. The full excitation and emission spectra for SYBR Safe DNA gel stain are provided online and can also be found in the protocol.

Can I use the SYBR Safe stain with my ethidium bromide filter and camera settings?

Some ethidium bromide filters allow the transmission of all light above 500 nm. These filters (which are often yellow in color) and their associated camera settings can be used with SYBR Safe DNA gel stain, usually with only minor adjustments to the exposure or gain. Other ethidium bromide filters (often red in color) only transmit light around or above 600 nm; these filters and their associated camera settings are not suitable for use with SYBR Safe DNA gel stain.

What are the recommended photographic settings for my gel documentation system when using SYBR Safe stain?

Stained gels can be photographed using Polaroid 667 black-and-white print film and SYBR Safe photographic filter (Cat. No. S37100). Invitrogen SYPRO photographic filter (Cat. No. S6656) or a Kodak Wratten #9 filter also work well. Table 5 in the SYBR Safe product manual lists a filter selection guide for different instruments.

What is the recommended filter for my gel documentation system when using SYBR Safe stain?

Please see the SYBR Safe home page for a list of recommended filters and settings for several different gel documentation instruments. You can find it by searching "SYBR Safe DNA Gel Stain" from the Thermo Fisher Scientific website home page.

If your system is not listed, please contact the instrument manufacturer for a recommendation. Note that the excitation and emission spectra of SYBR Safe gel stain are very similar to those of SYBR Green I, SYBR Green II, and SYBR Gold gel stains, as well as fluorescein (FITC). Therefore, filters appropriate for these dyes can also be used.

How do I use the SYBR Safe photographic filter?

The SYBR Safe photographic filter (Cat. No. S37100) is a Wratten #9 gelatin filter. This filter is a 75 mm x 75 mm sheet of plastic that should be mounted in front of the lens of the camera. With a Polaroid camera and B&W film (#667), the filter may be taped inside the hood or mounted in a cassette and snapped in place inside the hood (the opening in which the camera lens is mounted upon).

For other camera systems, this sheet may be mounted in a cassette or filter-housing and placed in front of the camera lens. An alternative is to use thread-on glass filters of the same rating available from most camera supply vendors. Please note - not all camera systems require use of the SYBR Safe filter. See the SYBR Safe home page for a list of recommended filters and settings for several different instruments - you can find the page by searching "SYBR Safe DNA Gel Stain" from theThermo Fisher Scientific website home page.

Can DNA bands stained with SYBR Safe be seen on a UV transilluminator without the use of emission filters?

DNA bands stained with SYBR Safe stain may be visible by eye on a 300 nm transilluminator if there is a sufficient amount of DNA per band. However, optimal detection is obtained by photographing the gel using a Wratten #9 emission filter (or other filter with a similar rating) with your CCD or film camera. With UV transilluminators (light boxes), UV bulbs may also emit some infrared (IR) wavelengths; if your camera lens is not specially coated to block IR, an IR-blocking filter is needed to prevent the appearance of the UV bulbs under your gel.

I work in an institution/city/state/country that requires additional tests to allow me to dispose of the SYBR Safe stain down the drain. Will your company perform these tests?

SYBR Safe DNA gel stain was tested extensively by four independent testing laboratories. The white paper "SYBR Safe DNA Gel Stain: Assessment of mutagenicity and environmental safety" may be downloaded from our website on the SYBR Safe informational page, which you can find by searching "SYBR Safe DNA Gel Stain" from the Thermo Fisher Scientific website home page.

Where can I find more safety information about SYBR Safe stain?

You can find information about all of our latest testing results on the SYBR Safe home page, which you can find by searching "SYBR Safe DNA Gel Stain" from the Thermo Fisher Scientific website home page.

Is SYBR Safe stain really safe? Do I have to use gloves when I use it?

In numerous tests carried out by independent, licensed testing laboratories, SYBR Safe stain showed little or no genotoxicity and no acute toxicity. This stain is not classified as hazardous waste under U.S. federal regulations. However, please exercise common safe laboratory practice when using this reagent - wearing gloves is still recommended. For more information on safety testing of the SYBR Safe stain, please visit our main SYBR Safe informational page, which you can find by searching "SYBR Safe DNA Gel Stain" from the Thermo Fisher Scientific website home page.

How should I dispose of SYBR Safe DNA Gel Stain and E-Gels containing SYBR Safe DNA Gel Stain?

Some institutions and municipalities have approved the disposal of SYBR Safe DNA Gel Stain directly into their waste water systems and regular trash receptacles. However, disposal regulations vary; please contact your safety office or local municipality for disposal guidelines. For more information on environmental testing and safety standards for SYBR Safe stain, please visit our main SYBR Safe informational page, which you can find by searching "SYBR Safe DNA Gel Stain" from the Thermo Fisher Scientific website home page.

Is SYBR Safe DNA gel stain available in both TBE and TAE buffers?

Yes, it is available in both buffers. The catalog numbers are as follows:
Cat. No. S33111 SYBR Safe DNA gel stain in 1X TAE
Cat. No. S33100 SYBR Safe DNA gel stain, 1L in 1X TBE
Cat. No. S33101 SYBR Safe DNA gel stain, 4L in 1X TBE
Cat. No. S33110 SYBR Safe DNA gel stain Starter Kit, includes 1L SYBR Safe DNA gel stain (Cat. No. S33100) in 1X TBE and one photographic filter (Cat. No. S37100)

Can gels be cast directly in the SYBR Safe DNA gel stain?

Yes, the agarose can be prepared directly in the SYBR Safe DNA gel stain (it may be heated in microwave). Run the gel normally, no destaining is required.
*Note: SYBR Safe DNA gel stain is prepared 0.5X TBE buffer. Use this preparation directly when making up a gel. Gels that include SYBR Safe DNA gel stain can be run in 0.5X or 1X TBE buffer without effects on resolution.

What are the benefits of the SYBR Safe DNA gel stain as compared to ethidium bromide?

SYBR Safe DNA gel stain was developed specifically for reduced mutagenicity to be safer than ethidium bromide for staining DNA in agarose or acrylamide gels. SYBR Safe DNA gel stain is not only less mutagenic than ethidium bromide, but its detection sensitivity is better than that of ethidium bromide.

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