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Electrophoresis in Southern and Northern blotting involves separating nucleic acids from a sample in a gel (usually agarose), based upon the molecular weight or structure of the nucleic acids.
Gels can be stained with, for example, ethidium bromide and viewed under UV light to examine the quality and quantity of separated components before proceeding. Standards are usually included in one lane to enable sizing of the separated fragments.
Genomic DNA is often cleaved using restriction enzymes to give smaller fragments that can be separated in the gel, and can be readily transferred from the gel to the membrane in the blotting step. DNA may also be fragmented after the electrophoresis step (see Blotting).
Separation is usually performed in agarose gels containing a denaturing agent such as formaldehyde or glyoxal/DMSO, which limits secondary structure that would otherwise disturb the separation by size. Fragmented RNA or microRNAs may also be separated using polyacrylamide gels followed by Northern blotting.
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