The Extraction and Isolation of DNA from Gels

As will be evident from a number of the following chapters (i.e., Chapters 31 , Chapters 38 –Chapters 41 , Chapters 51 –Chapters 53 ), gel electrophoresis of DNA is a widely used technique in molecular biology. In a number of cases, e.g., for such procedures as cloning and DNA sequencing, it is not sufficient just to analyze the DNA on these gels; the DNA must also be recovered from the gel. It is clear that the DNA in these cases has to be recovered in as high yields as possible and that the molecules should not be damaged. There are many published procedures for extracting DNA fragments from agarose or acrylamide gels (1 –4 ), but none are very satisfactory. As mentioned in Chapters 38 –Chapters 41 , agarose inhibits a number of enzymes used for labeling DNA molecules, for restriction, and for ligation. Acrylamide does not seem to inhibit most enzymes, but interferes with the electron microscopy of DNA. The procedures described below have all been used in our laboratory, albeit with varying degrees of success. The fact that a number of methods have not been included in this chapter does not mean that the particular method could not be of any use, but only that the authors are not familiar with it.The first step in each method is to locate the band of interest, either by staining the DNA with ethidium bromide or, if the DNA is radioactively labeled, by identifying by autoradiography, both of which are described elsewhere in this book and are therefore omitted from this chapter.