Agarose Gel Electrophoresis of DNA and RNA - Uses and Variations

Agarose electrophoresis is used for a variety of purposes. Specialty grades of agarose have been developed to fulfill specific requirements. The most commonly used variant is low-melting agarose, which has been modified to lower its melting temperature from over 90°C to around 65°C. This allows bands to be excised from a gel and then melted at a mild temperature to release the DNA. Although low melt agarose generally produces gels which are difficult to work with because of low mechanical strength, National Diagnostics' AquaPor LM, has exceptionally high strength, and produces gels which can be handled easily without breaking.

Another popular form of agarose has been modified to give increased mechanical strength to the gel. National Diagnostics' AquaPor ES is high quality agarose modified in this way. This is particularly useful when extra large DNA fragments are run. The low percentage gels required to run megabase fragments of DNA are extremely flimsy. Extra strength agarose allows the use of very low percentage gels, permitting the analysis of even larger pieces of DNA.

Finally, agarose can be refined to give matrices with enhanced resolution of small fragments, such as National Diagnostics' AquaPor HR. Standard agarose will give only about 5% size resolution; that is, to be resolved two fragments must differ by at least 5%. High resolution agarose can resolve fragments which differ by as little as 2%. This allows the resolution of fragments below 500bp, and is ideal for analyzing PCR products.

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