Novex™ TBE Gels, 6%, 10-well, 10 Gels/Box - FAQs

Can I stain my TBE gel? How?

Yes, you can stain your TBE gels with ethidium bromide, SYBR Green I, SYBR Green II, and the SilverXpress Silver Staining Kit. For ethidium bromide staining, soak the gel in a 2 µg/mL solution of ethidium bromide in ultrapure water for 20 minutes. Destain by rinsing with three successive 10-minute rinses of ultrapure water. Visualize bands under UV light.

What is the difference in composition between the Invitrogen 6% TBE Gels and the Invitrogen 6% DNA Retardation Gels?

The Invitrogen 6% DNA Retardation Gels contain 0.5X TBE. Both gels will work for gel retardation; however, the 1X TBE in the Invitrogen 6% TBE Gels have a higher ionic environment, which may affect DNA-protein interactions. The 0.5X TBE used in the Invitrogen 6% DNA Retardation Gels usually works better, as it offers good fragment separation in electrophoresis yet has an ionic strength low enough to promote DNA-protein interactions.

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What are the smallest fragments that can be visualized on the TBE gels?

On the Invitrogen 10% TBE gels, a 51 bp marker can be clearly seen. On the Invitrogen 20% TBE gel, the 18 and 12 bp markers can be clearly seen.

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What is the concentration of EDTA in the TBE gels? How about glycerol?

The EDTA concentration in our TBE gels is 0.06% (w/v). The 20% TBE gels contain 4% glycerol for maximal resolution. All other TBE gels contain 0.8% glycerol in a layer that represents the bottom 9% of the gel. There is no glycerol in the rest of the gel.

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Can I stain my TBE gel or my TBE-urea gel? How?

Yes, for ethidium bromide staining, soak the gel in a 2 µg/mL solution of ethidium bromide in ultrapure water for 20 minutes. Destain by rinsing with three successive 10-minute rinses of ultrapure water. Visualize bands under UV light

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What should the running conditions be for the TBE gels (voltage, current, run time, etc.)?

Voltage: 200 V constant*
Approximate current at start: 10-18 mA/gel
Approximate current at end: 4-6 mA/gel
Run time: Approximately 30-90 minutes, dependent on gel percentage. The run is complete when the bromophenol blue (darker) tracking dye reaches the bottom of the gel.

* Voltages up to 250 V may be used to reduce run time.

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What are the TBE gel specifications, specifically the gel size and cassette size?

Please see the gel specifications below:

Gel matrix: Acrylamide/bis-acrylamide
Gel thickness: 1.0 mm and 1.5 mm
Gel size: 8 cm x 8 cm (height x width)
Cassette size: 10 cm x 10 cm (height x width)

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What are the shelf life and storage conditions for my TBE gels?

The shelf life is 8 weeks for the gels, which should be stored at 4°C.

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I am planning to use a TBE polyacrylamide gel for electrophoresis of my nucleic acid fragment. How do I know if the size of my fragment is suitable for a particular gel you offer?

To help you choose the TBE polyacrylamide gel that will provide optimal separation results for your nucleic acid fragment, we have designed gel migration charts for each gel type offered. Please check the TBE gel migration charts on page 74 of the Novex Pre-Cast Gel Electrophoresis Guide (https://tools.thermofisher.com/content/sfs/manuals/electrophoresisguide_man.pdf).

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How can I isolate DNA from Thermo Fisher Scientific TBE and TBE-Urea gels?

Here is the protocol you can follow:
(1) Run the gel. Locate the DNA of interest by autoradiography or by examination of ethidium bromide stained gels.
(2) Use a razor blade to cut out the upper 1/2 to 2/3 of the band of interest.
To recover a fragment of DNA identified by autoradiography, cut out from the X-ray film a small rectangle encompassing the image of the fragment. Align the film over the gel and cut out the segment of polyacrylamide bordered the rectangular hole in the film.
(3) Transfer the gel slice to a microcentrifuge tube. Use a sterile glass rod to crush the slice against the wall of the tube.
(4) Calculate the volume of the slice and add 1 to 2 volumes of elution buffer to the microcentrifuge tube.
Elution buffer: 0.5 M ammonium acetate, 10 mM magnesium sulfate, 1 mM EDTA (pH 8.0), 0.1% SDS
It is convenient if the volume of elution buffer is no greater than 0.5 mL since the eluted fragment of DNA can then be precipitated with ethanol in a single tube.
(5) Close the tube and incubate at 37 degrees C on a rotary platform. Small fragments of DNA (500 bases) are eluted in 3 to 4 hours.
(6) Centrifuge the sample at 12,000 g for 1 minute at 4 degrees C in a microcentrifuge. Transfer the supernatant to a fresh microcentrifuge tube, being careful to avoid transferring fragments of polyacrylamide.
(7) Add additional 0.5 mL volume of elution buffer to the pellet of polyacrylamide, vortex briefly, and re-centrifuge. Combine the two supernatants.
(8) Remove any remaining fragments of polyacrylamide by passing the supernatant through a disposable plastic column or a syringe barrel containing Whatman GF/C filter or packed siliconized glass wool.
(9) Add 2 volumes of ethanol at 4 degrees C and store the solution on the ice for 30 min. Recover the DNA by centrifugation at 12,000 g for 10 min at 4 degrees C in a microcentrifuge.
(10) Re-dissolve the DNA in 200 µL of Tris-EDTA (TE) buffer (pH 7.6), add 25 µL of 3M sodium acetate (pH 5.2) and re-precipitate the DNA with 2 volumes of ethanol as described in step 9. TE Buffer (pH 7.6): 10 mM Tris HCl (pH 7.6), 1mM EDTA (pH 8.0).
(11) Carefully rinse the pellet once with 70% ethanol and redissolve the DNA in TE buffer (pH 7.6) to a final volume of 10 µL.
(12) Check the amount and the quality of the fragment by polyacrylamide gel electrophoresis.

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What's the difference in composition between the 6% TBE gels and the 6% DNA retardation gels?

The 6% DNA retardation gels are 0.5X TBE. Both gels will work for gel mobility shift assays, but the 1X TBE has a higher ionic environment that may affect DNA/protein interactions. 0.5X TBE usually works better.

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What can be used to stain Invitrogen precast TBE-Urea or TBE gels?

(1) Ethidium bromide: Soak gel in a 2 µg/mL solution of ethidium bromide in ultrapure water for 20 min. Destain by rinsing with three successive 10-min rinses of ultrapure water. Visualize bands under UV light. The gel must be removed from the cassette prior to visualization of the DNA under a UV light. Because polyacrylamide quenches the fluorescence of ethidium bromide, it is not possible to detect bands that contain less than about 10 ng of DNA by this method. SilverXpress and SYBR stains will provide greater detection sensitivity.

(2) Invitrogen SilverXpress Stain: Follow the standard procedure from the instruction booklet for staining TBE or TBE-Urea gels.

(3) SYBR Green I/II Nucleic Acid Gel Stain: See the SYBR Green Staining Manual for protocol details.

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(1) Ethidium bromide: Soak gel in a 2 µg/mL solution of ethidium bromide in ultrapure water for 20 min. Destain by rinsing with three successive 10-min rinses of ultrapure water. Visualize bands under UV light. The gel must be removed from the cassette prior to visualization of the DNA under a UV light. Because polyacrylamide quenches the fluorescence of ethidium bromide, it is not possible to detect bands that contain less than about 10 ng of DNA by this method. SilverXpress and SYBR stains will provide greater detection sensitivity.

(2) SilverXpress Stain: Follow the standard procedure from the instruction booklet for staining TBE or TBE-Urea gels.

(3) SYBR Green I Nucleic Acid Gel Stain (Cat. No. S7585)/SYBR Green II RNA Gel Stain (Cat. No. S7564): See the SYBR Green Staining Manual for protocol details.

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For the purpose of recovering and solubilizing nucleic acids in alcohol, can TAE running buffer be used instead of TBE running buffer when running a pre-cast TBE gel?

A TAE running buffer used in conjunction with a TBE gel would create high current and may lead to gel hydrolysis. Also, the acetate ion in TAE migrates faster than the borate ion in TBE buffer, and can create fuzzy bands. It is possible to try soaking the TBE gel (run in TBE buffer) in the TAE buffer following the run and then eluting from that. Since nucleic acids diffuse out of the gel relatively slowly, this may work.

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What are the smallest fragment sizes that can be visualized on TBE gels?

On the Invitrogen 10% TBE gel, the 51-bp marker from the Boehringer Mannheim DNA MW V Kit can be clearly visualized. On the Invitrogen 20% TBE gel, the 18- and 12-bp markers from the same kit can be clearly seen at 2 micrograms total DNA loaded.

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What is the recommended maximum sample loading volume for Novex TBE and TBE-Urea gels?

The recommended maximum sample loading volumes for Novex TBE and TBE-Urea gels are shown below:

10-well gels: 25 µL
12-well gels: 20 µL
15-well gels: 15 µL

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Are Novex TBE Gels compatible with Bio-Rad mini gel tanks?

No. Our precast Novex TBE Gels are not compatible with Bio-Rad mini gel tanks. They are only compatible with either our Mini Gel Tank (Cat. No. A25977) or the XCell SureLock Mini Cell (Cat. No. EI0001).