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View additional product information for SYBR™ Safe DNA Gel Stain in 1X TAE - FAQs (S33111, S33112)
42 product FAQs found
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.
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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.
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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.
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SYBR Safe DNA Gel Stain is easily removed from nucleic acids by ethanol precipitation.
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We strongly discourage the reuse of SYBR Safe DNA Gel Stain, as this practice significantly lowers sensitivity.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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The SYBR Safe DNA Gel Stain content in a 1X solution is less than 1 ppm.
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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.
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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 (Cat. No. S33102) was specifically developed as a safer alternative to ethidium bromide. SYBR Green I (Cat. No. S7585) is an ultrasensitive stain for dsDNA, and SYBR Green II (Cat. No. S7564) is a highly sensitive stain for RNA and ssDNA. All SYBR dyes are optimally excited by the Safe Imager Blue-Light Transilluminator.
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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).
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Disposal regulations vary. Please contact your safety office or local municipality for disposal guidelines.
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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
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Yes, SYBR Safe stain is easily removed from nucleic acids by ethanol precipitation or by the ethanol wash steps used for purification spin columns.
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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.
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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.
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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.
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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.
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We strongly discourage the reuse of SYBR Safe stain, as this practice significantly lowers sensitivity.
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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.
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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.
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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.
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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.
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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.
Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.
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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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)
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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.
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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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