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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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The McGraw Hill Companies, 2001
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DNA Sequencing
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ity that chain termination will occur at every appropriate position. If the dideoxynucleotide were added in place of the deoxynucleotide, then the chain would be terminated the rst time the complement of that base appeared in the template strand. By mixing the dideoxynucleotides and the deoxynucleotides, we are assured that termination will occur in every appropriate position. In gure 13.32c, we see that the template has two adenines. Therefore, in the ddTTP reaction mixture, adenine s complement (thymine) is needed twice. There are
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thus two possible points for ddTTP to incorporate, two possible chain terminations, and therefore two fragments that could end in dideoxythymidine, of two and seven bases, respectively. Similarly, there are three possible fragments ending in adenine, of one, three, and eight bases; three ending in cytosine, of four, ve, and nine bases; and one ending in guanine, of six bases ( g. 13.32c and g. 13.33, top). After DNA synthesis is completed, the old primer is removed, leaving only newly synthesized DNA fragments ( g. 13.33). Newly replicated segments of various lengths
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Isolate newly synthesized DNA
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Figure 13.33 Electrophoresis of segments produced by the dideoxy method of
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DNA sequencing. This method allows direct reading of the sequence. The asterisks indicate the dideoxynucleotides. The newly synthesized reaction products seen in gure 13.32 are isolated by removal of the primer and template. Each reaction mixture (e.g., ddTTP is the mixture containing dideoxythymidine triphosphates) produces speci c products of speci c lengths that can be determined by electrophoresis. In the case of the ddTTP mixture, two fragments ending in thymine are possible; one is two bases long, the other seven bases long. Thus, the complement of thymine, adenine, appears in positions 2 and 7 of the original piece of DNA. However, either the original strand or its complement (the new synthesis) yields the original sequence since DNA is a double helix; the sequence in one strand is always de ned by the complementary sequence in the other strand.
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Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
13. Genomics, Biotechnology, and Recombinant DNA
The McGraw Hill Companies, 2001
Thirteen
Genomics, Biotechnology, and Recombinant DNA
from each reaction mixture are placed in separate slots and then electrophoresed on polyacrylamide gels to determine the lengths of the segments. Since only newly synthesized DNA segments are radioactive, autoradiography lets us keep track of newly synthesized DNA. As you can see from the autoradiograph of the gel in gure 13.33, each subsample produces segments that begin at the primer con guration (beginning of synthesis) and end with the chain-terminating dideoxy base. By starting at the bottom and reading up, back and forth across the gel, we can directly determine the exact sequence of the DNA segment. Because they have the appearance of stepladders in each lane ( g. 13.34), the gels are usually referred to as stepladder gels or ladder gels. This technique (in the form of the original plus-andminus method) was rst used to sequence the genome of the DNA phage X174 (box 13.3). That phage was used because it lent itself to the sequencing method. It has single-stranded DNA within the phage coat, yet its DNA becomes double-stranded once it enters the bacterium. Creating a primer con guration was thus relatively easy. The double-stranded circle from within the host could be treated with a restriction endonuclease to produce double-stranded fragments ( g. 13.35). These fragments could then be denatured. From this mixture, a particular fragment could be isolated by electrophoresis. The isolated strand would reanneal to the single-stranded DNA taken from the phage heads, forming a primer for new growth. The same restriction endonuclease would free the new growth after it had taken place. Thus, the dideoxy method was relatively easy to apply to the 5,387base chromosome of X174.
Creating a General-Purpose Primer
To make the dideoxy method ef cient, researchers created a general primer for routine sequencing work by recombinant DNA engineering of an E. coli vector, the single-stranded DNA phage M13. This phage is similar to X174 in that both are packaged as single-stranded DNA, and both are replicated to double helices within the host. Therefore, the double-stranded form within the host, called the replicating form, can be engineered by standard methods, and the single-stranded form can be used for sequencing. The system works as follows. By very clever engineering, J. Messing and his colleagues created cloning sites for a variety of restriction enzymes in a bacterial gene (lacZ) that had been inserted into M13 ( g. 13.36). The gene is for the -galactosidase enzyme that normally breaks down lactose. It also breaks down an arti cial substrate of the enzyme, X-gal, which is normally colorless. When cleaved by -galactosidase, X-gal becomes blue. Thus, in the presence of the functional lacZ gene, M13 plaques are blue. If the gene is disrupted by a cloned insert, X-gal does not break down,
A G G A T T T A A C A C G G A C G A T A G G A T C G G C G A T C G A T C G G C T G T A G T G G A A A G A T T Figure 13.34 Autoradiograph of a dideoxy sequencing gel. The
letters G, A, T, and C along the bottom refer to the ddGTP, ddATP, ddTTP, and ddCTP reaction mixtures, respectively. Lanes are repeated for easier identi cation of the bands. The sequencing is also veri ed by sequencing the complementary strand and checking for agreement. (Courtesy of Richard J.
Roberts.)
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