Analysis of DNA by Southern Blotting

Southern transfer and hybridization are used to study how genes are organized within genomes by mapping restriction sites in and around segments of genomic DNA for which specific probes are available. Genomic DNA is first digested with one or more restriction enzymes, and the resulting fragments are separated according to size by electrophoresis through a standard agarose gel. The DNA is then denatured in situ and transferred from the gel to a solid support (usually a nylon or nitrocellulose membrane). The DNA attached to the membrane is hybridized to a labeled DNA, RNA, or oligonucleotide probe, and bands complementary to the probe are located by an appropriate detection system (e.g., by autoradiography). By estimating the size and number of the bands generated after digestion of the genomic DNA with different restriction enzymes, singly or in combination, it is possible to place the target DNA within a context of restriction sites.