2X RNA Loading Dye is recommended for preparation of RiboRuler RNA ladders and RNA samples for electrophoresis on agarose or polyacrylamide gels. In most denaturing agarose gel systems bromophenol blue migrates slightly faster than human 5S rRNA, whereas xylene cyanol FF migrates slightly slower than 18S rRNA.
- Tracking dyes bromophenol blue and xylene cyanol FF
- Intercalating dye ethidium bromide
- Formamide—a denaturing agent which allows RNA fragments to separate according to size even during non-denaturing electrophoresis and acts as an RNA stabilizer
Agarose is a non-toxic polysaccharide extracted from seaweed. It is easy to use and is relatively inexpensive. For electrophoresis, high-quality agarose is crucial in order to obtain sharp bands. Standard high melting point agarose is used in routine DNA electrophoresis for separation of a wide range of DNA fragments. Low melting/gelling temperature agarose is recommended for rapid DNA gel extraction with the agarose digesting enzyme Agarase. It also commonly used for "in-gel" DNA treatment with enzymes or for bacterial transformation with nucleic acids directly after re-melting the gel.
Today you even have the convenience to use agarose in tablet format to omit messy weighing when preparing your gels. Try Thermo Scientific™ TopVision Agarose Tablets: high-quality, multipurpose agarose tablets in blister packaging.
Comparison of TopVision Agarose Tablets to traditional agarose powder
|Traditional agarose powder||TopVision Agarose Tablets||Advantage with TopVision Tablets|
|Gel-to-gel variation||High variability from weighing step||Tablet form delivers higher consistency hand cast gel performance||Consistent results|
|Hands-on time||Time consuming weighing step||<1 min. hands-on time— eliminate weighing step completely||Time-saving|
|Manufacturing process||Heavy dependency and use of organic solvents such as methanol, acetonitrile, DMF, heptane, etc.||Organic solvent-free process—complete elimination of any organic solvent use||Reduced environmental impact|
|Packaging||Plastic bottles||Tablet blister—bottle-free packaging, enhanced convenience and portability||Convenient|
RNA molecules can be analyzed on both native or denaturing agarose and polyacrylamide gels. Non-denaturing RNA electrophoresis eliminates the need for hazardous chemicals, but due to intramolecular interactions, RNA molecules can form extensive double-stranded structures that are quite difficult to disrupt. As a result, accurate sizing of RNA molecules is not always possible under non-denaturing conditions. Native RNA electrophoresis is therefore typically used to assess the overall quality of total RNA. Denaturing electrophoresis is recommended to precisely determine the size and integrity of RNA molecules.
Non-denaturing RNA Electrophoresis
|Size of RNA||Product||Size||Catalog #|
|>1,500 bp||50X TAE Buffer (Tris-acetate-EDTA)||1 L||B49|
|<1,500 bp||10X TBE Buffer (Tris-borate-EDTA)||1 L||B52|
Denaturing RNA Electrophoresis
Types of denaturing RNA electrophoresis conditions include:
- Denaturing polyacrylamide gel electrophoresis in TBE buffer supplemented with 7 M urea
- Formaldehyde agarose gel electrophoresis in MOPS buffer
- Glyoxal/DMSO agarose gel electrophoresis in sodium phosphate buffer
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