Novex™ TBE-Urea Gels, 6%, 12-well, 10 Gels/Box - FAQs

我进行TBE-尿素凝胶电泳时出现了高背景和拖尾条带。我应该如何才能解决这一问题？

这里有一些对您实验的建议：

•RNA样本可能被RNA酶降解了。遵循标准注意事项以避免污染。
•确保在上样前对样本在70°C加热3分钟。如果没有这样做，则寡核苷酸不会被完全变性，导致出现拖尾。
•确保在上样前彻底将尿素冲洗出上样孔。尿素会持续从凝胶渗入上样孔内。尿素很浓而且会使样本形成球状。
•上样体积超过10 µL可能引起拖尾。这一体积比琼脂糖凝胶所用的上样体积小。
•如果没有使用超纯水（18毫欧姆），则可能出现拖尾条带和高背景。
•检查电泳缓冲液和上样缓冲液是否正确制备和稀释。
•确保使溴酚蓝染料迁移到达边缘。过早停止电泳可能导致电泳效果较差。

Invitrogen TBE-尿素系统可以使用含有福尔马林的上样缓冲液吗？

该系统可以使用多种上样缓冲液配方；但是，我们发现根据上样缓冲液的不同，电泳条带的形态会有很大的不同。在评估了尿素、福尔马林以及各种缓冲液系统之后，我们发现使用尿素、Ficoll和TBE缓冲溶液能获得最清晰、最整齐的条带。使用含福尔马林的上样缓冲液将得到模糊、不清晰的条带。

我可以对TBE凝胶或TBE-尿素凝胶染色吗？如何染色？

可以，对于EB染色，将凝胶在超纯水配制的2 µg/mL EB溶液中浸泡20分钟。接下来使用超纯水进行3次洗涤脱色，每次10分钟。在紫外光下观察条带。

I am getting high background and smeared bands on my TBE-urea gels. What should I do?

Here are some suggestions for your experiments:

- The RNA samples may have been degraded by RNases. Use standard precautions to prevent contamination.
- Make sure samples are heated for 3 minutes at 70°C just prior to loading. If this is not done, the oligonucleotides will not be fully denatured, which may result in a smeared background.
- Be sure to vigorously flush urea out of sample wells just prior to loading the sample. Urea will continually seep from the gel into the well. Urea is very dense and will force the sample into a ball.
- A sample volume over 10 µL may result in smearing. This volume is less than may be used with agarose gels.
- If ultrapure water (18 milliohms) is not used, smeared bands and high background may result.
- Check to make sure the running and sample buffers have been prepared and diluted correctly.
- Make sure to run the bromophenol blue until it reaches the slot. Stopping the run short can result in less than optimal results.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

Can I use a sample buffer containing formamide with the Invitrogen TBE-urea system?

There are many sample buffer formulations used; however, we have found a distinct difference in the band appearance depending on the sample buffer composition. After evaluating urea, formamide, and various buffer systems, we found that the sharpest, flattest bands were obtained with a urea, Ficoll, and TBE buffer solution. Sample buffers made with formamide provided fuzzy, indistinct bands.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

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

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

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).

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

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.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

What precast gel can I use for RNase protection assays (RPA)?

The Invitrogen 6% TBE-Urea (denaturing) gels can be used for RNase protection assays.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

Can a sample buffer with formamide be used with the Invitrogen TBE-Urea system?

There are many sample buffer formulations used, however we have found a distinct difference in the band appearance depending on the sample buffer composition. After evaluating urea, formamide, and various buffer systems, we found that the sharpest, flattest bands were obtained with a urea, Ficoll, and TBE buffer solution. Sample buffers made with formamide resulted in fuzzy, indistinct bands.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

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.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

(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.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

What can be done to prevent abnormal band shapes (round bands instead of flat sharp bands) and poor resolution on a TBE-Urea Gel?

(1) Make sure urea is thoroughly flushed from sample wells just prior to loading samples. Urea will continuously diffuse into the wells and will force the sample into a ball, resulting in rounded bands rather than flat bands.

(2) Use the Invitrogen TBE-Urea sample buffer. We have found that our TBE-Urea sample buffer provides the sharpest, flattest bands on our gels.

(3) Load less sample onto the gel. For the flattest, sharpest bands and highest resolution, load between 0.16 and 0.33 µg (0.005 - 0.01 OD) per band. More than that will result in rounded bands.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

What prevents high background and smeared bands on TBE-Urea gels?

(1) If running RNA samples, the samples may have been degraded by RNases. Use standard precautions to prevent contamination.

(2) Make sure samples are heated for 3 min at 70 degrees C just prior to loading. If this is not done, the oligos will not be fully denatured and this may result in a smeared background.

(3) Be sure to vigorously flush urea out of sample wells just prior to loading the sample. Urea will continually seep from the gel into the well. Urea is very dense and will force the sample into a ball or out of the well.

(4) If the sample volume is over 10 microliters, this may result in smearing.

(5) If ultrapure water (18 megaOhm) is not used, smeary bands and high background may result.

(6) Check to make sure the running and sample buffers are prepared and diluted correctly.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

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.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

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.

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Purification and Analysis Support Center.

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

Find additional tips, troubleshooting help, and resources within our Nucleic Acid Gel Electrophoresis and Blotting Support Center.