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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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13. Genomics, Biotechnology, and Recombinant DNA
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Edwin M. Southern (1938 ). (Courtesy of Edwin Southern.)
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In a digest of this kind, however, there are usually so many fragments that the result is simply a smear of oligonucleotides, from very small to very large. To proceed further, we have to transfer the electrophoresed fragments to another medium for probing, or the DNA fragments would diffuse out of the agarose gel. Nitrocellulose lters or nylon membranes are excellent for hybridization because the DNA fragments bind to these membranes and will not diffuse out. The transfer procedure, rst devised by E. M. Southern, is called Southern blotting. In this technique, the double-stranded DNA on the agarose gel is rst denatured to single-stranded DNA, usually with NaOH.Then the agarose gel is placed directly against a piece of nitrocellulose lter, and the resulting sandwich is placed agarose-side-down on a wet sponge. Dry lter paper placed against the nitrocellulose side wicks uid from the sponge, through the gel, and past the nitrocellulose lter, carrying the DNA segments from the agarose to the nitrocellulose ( g. 13.13). NaOH is used as the transfer solution in the tray.The DNA digest fragments are then permanently bound to the nitrocellulose lter by heating. DNA-DNA hybridization takes place on the lter. (A similar technique can be performed on RNA, which is called, tongue-in-cheek, northern blotting. Immunological techniques, not involving nucleotide complementarity, can be used to probe for proteins in an analogous technique called western blotting.) A labeled probe can be obtained in several different ways. In this example, the easiest way to obtain a radioactive probe would be to isolate -globin messenger RNA from rabbit reticulocytes and construct cDNA using the reverse-transcriptase method described.The deoxyribonucleotides used during reverse transcription are then synthesized to contain radioactive phosphorus, 32P. As gure 13.12 shows, after hybridization, a single radioactive band locates a DNA segment with the -globin gene. Note that the probe, originating from messenger RNA, will lack the introns present in the gene. However, probing is successful as long as there are complementary regions in the two nucleotide strands.
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Arrangement of gel and lters in the Southern blotting technique. The NaOH buffer is drawn upwards by the dry lter paper, transferring the DNA from the agarose gel to the nitrocellulose lter.
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To clone the -globin gene, a second agarose gel would be run with a sample of the digest used in gure 13.12. That gel, not subject to DNA-DNA hybridization, would have the -globin segment in the same place. The band, whose location is known from the autoradiograph, could be cut out of the agarose gel to isolate the DNA. We could then clone the DNA by methods discussed earlier in the chapter.
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Probing for a Cloned Gene
Dot Blotting
The methods we have described are also useful in locating genes already cloned within plasmids, for example, after a genomic library has been constructed. In this case, electrophoresis and Southern blotting are not needed since we will be probing for a particular sequence of DNA already cloned rather than DNA segments within a digest. For example, the DNA of a human-mouse hybrid cell line was cloned in order to locate human DNA. In this case, a hybrid cell line had only one human chromosome, chromosome 20. In order to locate DNA from that chromosome, probes were used that were isolated from human chromosomes. The probes were radioactively labeled. Meanwhile, 288 E. coli colonies, each containing a hybrid plasmid, were grown and transferred directly to a nitrocellulose lter. In preparation for probing, the cells were lysed and their DNA denatured. The plasmid DNA within the cells of each clone was then hybridized with the radioactive probes. Figure 13.14 is an autoradiograph of the 288 clones.The two dark spots indicate clones car-
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