Electrophoresis of DNA

The cut DNA is size-fractionated by gel electrophoresis and the choice of separation matrix is determined by the sizes of the DNA fragments. For most applications, agarose is the matrix of choice because of its ease of use. For fragments smaller than a few hundred base pairs, acrylamide has been used because of its greater resolving power but acrylamide gels pose practical problems at the blotting stage. In recent years, specialist agaroses have been developed with much improved resolution of small DNA fragments. Conventional agarose gel electrophoresis is incapable of resolving DNA fragments larger than -15 kb and for such fragments it is often necessary to use field inversion gel electrophoresis (FIGE) or pulsed field gel electrophoresis (PFGE). The latter is capable in some instances of separating intact chromosomes.

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