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E-Gel 96 High-Throughput Agarose Electrophoresis System Manual / Product Insert

  • Version: Version I, 18 April 2005
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User Guide: Alkaline Agarose Gel Electrophoresis Manual / Product Insert

  • Version: Jan. 2015
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User Guide: Non-denaturing Agarose Gel Electrophoresis Manual / Product Insert

  • Version: Jan. 2015
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What amount of ethidium bromide do I need to stain nucleic acids in gels? Product FAQ

Answer

After electrophoresis, the gel should be stained in a 0.5-1.0 µg/mL solution of ethidium bromide in deionized water for 15 to 60 min depending on the thickness of the gel. As an optional step to reduce background fluorescence, the gel can be destained in deionized water for 15 to 30 min. Alternatively, ethidium bromide may be added directly to the agarose prior to casting. Add ethidium bromide to melted agarose to a final concentration of 0.5 µg/mL. This has the advantage of reducing the amount of ethidium bromide waste. However, this procedure may reduce the migration rate of nucleic acids.

Answer Id: E3069

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What is the best way to analyze RNA that I've isolated using a RiboMinus kit? Product FAQ

Answer

The purified RNA is easily quantitated using UV absorbance at 260 nm or a Quant-iT RNA Assay Kit. To verify rRNA depletion, electrophorese your sample on an agarose gel or use an Agilent 2100 Bioanalyzer. Agarose gel electrophoresis should show depletion of 18S and 28S rRNA bands compared to a control sample. Absence of contaminating DNA and RNA degradation may also be confirmed by agarose gel electrophoresis. The efficiency of rRNA depletion in the purified RNA, RNA degradation, and RNA concentration can also be analyzed using a bioanalyzer.

Answer Id: E7895

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How important is the quality of my DNA template in long PCR? Product FAQ

Answer

Template preparation becomes particularly important when performing longer amplifications (>15 kb). Therefore, it is recommended to check the length of the DNA by agarose gel electrophoresis.

Answer Id: E8676

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I ran my DNA molecular weight ladder, and several bands seem to be missing. Can you offer suggestions on how to rectify this? Product FAQ

Answer

There are a few possible reasons for this:

(1) Small DNA bands were electrophoresed off the gel. Electrophorese the gel for less time, at lower voltage, or use a higher percentage gel.

(2) The small bands migrated with the dye front due to differences in ionic strength between gel and buffer. Be sure the buffer in the gel is the same as the electrophoresis buffer.

(3) DNA bands of similar molecular size were not resolved. Increase the electrophoresis time and check the proper percentage gel for resolution. For DNA fragments <1,000 bp, try Agarose 1000 (Cat. No. 16550100) instead of agarose.

(4) DNA was denatured. Do not heat standards (except Lambda-derived markers) prior to electrophoresis. Dilute markers in a buffer containing 20 mM NaCl.

Answer Id: E3990

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Is E-Gel software compatible with Windows 10? Product FAQ

Answer

Yes, both the E-Gel GelCapture Acquisition Software and E-Gel GelQuant Express Analysis Software applications are compatible with Windows 10; however, the E-Gel GelQuant Express Analysis Software will require the purchase of an E-Gel Imager Quantitation USB dongle (Cat. No. 4466610):
https://www.thermofisher.com/order/catalog/product/4466610

Please visit the following link (https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/nucleic-acid-gel-electrophoresis/e-gel-electrophoresis-system/e-gel-imager-system/e-gel-software.html) and follow the instructions to download the software.
Note: Please make sure that you download the correct version of the E-Gel GelCapture Software based on the serial number of your instrument.

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

Answer Id: E18627

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I transfected my bacmid DNA but saw no signs of infection. The quality of my DNA prep might be an issue. How can I analyze the bacmid DNA? Product FAQ

Answer

We recommend running 1/8th of the 40 µL midiprep sample on a 0.5% TAE agarose gel. Electrophorese slowly at 23 V for 12 hr. The banding pattern of the recombinant bacmid midiprep should be seen.

Answer Id: E9441

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How does the CloneChecker system work? Product FAQ

Answer

The system contains sets of proprietary chemical solutions that release nucleic acids, especially plasmids, from bacterial cells. Typically, released plasmids are then characterized physically by supercoiled size or by restriction digestion pattern using agarose gel electrophoresis.

Answer Id: E3134

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How can I quantify my DNA after bisulfite conversion? Product FAQ

Answer

Checking your converted sample by O.D.260/280 tends to be inconsistent. We suggest performing qPCR or agarose gel electrophoresis and comparing your sample to a known amount of DNA to quantify your DNA after bisulfite conversion.

Answer Id: E5101

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What buffer should I use for my E-Gel agarose gel electrophoresis experiments? Product FAQ

Answer

The E-Gel agarose gel system is a precast bufferless TAE system that uses ion exchange matrices. The gels themselves are enclosed within a semi-UV-transparent cassette. This patented technology results in a sustained electric field with enhanced buffering capacity. E-Gel gels thus eliminate the need for you to prepare and dispose of liquid buffer, thus saving time and waste.

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

Answer Id: E7960

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Why does the Anza restriction enzyme come with a clear buffer and a red buffer? Product FAQ

Answer

When the next step following digestion is agarose gel electrophoresis, the Anza Red buffer can be used directly. The Anza Red buffer contains the necessary loading dye and density gradient for directly loading on to the agarose gel. The red dye does not interfere with digestion and helps reduce additional pipetting.

Use the clear Anza Buffer for applications that require analysis by fluorescence excitation, as the dyes in the Anza Red Buffer may interfere with some fluorescence measurements.

Answer Id: E13441

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With the Neon NxT Electroporation System, will a low A260/A280 ratio lead to both reduced transfection efficiency and cell viability? Product FAQ

Answer

Yes. To check the quality of your DNA, we strongly recommend confirming that both A260/A280 and A260/230 ratios are between 1.6 -2.0 and checking for DNA degradation by agarose gel electrophoresis.

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

Answer Id: E21645

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Will a low A260/A280 ratio lead to both reduced transfection efficiency and cell viability in the Neon device? Product FAQ

Answer

Yes. To check the quality of your DNA, we strongly recommend confirming both A260:A280 and A260/230 ratios are between 1.6-2.0 and check for DNA degradation by agarose gel electrophoresis.

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

Answer Id: E9004

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