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We now turn our attention to a major result of recombinant DNA technology, DNA sequencing. Recombinant DNA technology, with its ability to isolate and amplify small, well-de ned regions of chromosomes, has allowed the development of DNA sequencing techniques.
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Paul Berg of Stanford University, Walter Gilbert of Harvard University, and Frederick Sanger of the Medical Research Council in Cambridge, England, shared the 1980 Nobel Prize in chemistry. Berg won for creating the rst cloned DNA molecules when he spliced the SV40 genome into phage . Gilbert and Sanger were awarded the prize for independently developing methods of sequencing DNA. Gilbert, along with Allan Maxam, developed a method of DNA sequencing called the chemical method. It involves chemically breaking down the DNA at speci c bases. Sanger, who won a Nobel Prize in 1959 for sequencing the insulin protein, later took part in developing methods for sequencing RNA. His sequencing method, developed with Alan Coulson, involved DNA synthesis and was called the plus-and-minus method. The further development of the method by Sanger, Coulson, and S. Nicklen, using speci c chain-terminating nucleotides, led to a modi cation of the plus-and-minus method known as the dideoxy method.
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terminating nucleotides, stops DNA synthesis at known positions. These chain-terminating nucleotides are formed of sugars lacking OH groups at both the 2 and 3 carbons (hence the term dideoxy). Without a 3 -OH group, a dideoxynucleotide cannot be used for further DNA polymerization ( g. 13.31). Chain-terminating nucleotides permit synthesis to be stopped at a known base. The sample to be sequenced is elongated separately in four different reaction mixtures, each having all four normal nucleotides but also having a proportion of one of the chain-terminating dideoxy nucleotides. For example, if the pool of thymine-containing triphosphate nucleotides contains a portion of the dideoxythymidine triphosphate molecules, then synthesis of the growing strand is sometimes terminated when adenine (the complement of thymine) appears on the template, creating fragments that end in thymine. Similar
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Walter Gilbert (1932 ).
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Frederick Sanger (1918 ).
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(Courtesy of Dr. Frederick Sanger.)
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The Dideoxy Method
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In the dideoxy method, manipulation of DNA synthesis enables DNA sequencing. Remember from chapter 9 that DNA synthesis occurs at a primer con guration, one in which double-stranded DNA ends with a 3 -OH group on one strand. The other strand continues as single-stranded DNA ( g. 13.31, middle). The dideoxy method creates a primer con guration of the DNA to be sequenced and enables replication to proceed. A trick, using chain-
Figure 13.31 Dideoxy nucleotides cause chain termination
during DNA replication. The dideoxy primer con guration lacks the 3 -OH group needed for chain lengthening in a normal primer con guration.
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
reactions are carried out in separate test tubes for each of the other nucleotides, producing fragments that terminate when the respective complementary nucleotide is present. The resulting fragments from each reaction are electrophoresed, generating a pattern on the gel that reveals the sequence of the newly synthesized DNA. Let us go through an example. In gure 13.32a, we show the DNA to be sequenced, a small segment of nine base pairs. To sequence this segment, one must get one strand of this double-stranded segment into the con guration shown in gure 13.32b. The DNA to be sequenced must be the template for new
DNA synthesis. (We will soon discuss how we obtain the required con guration.) Having created the necessary primer con guration, we take four subsamples of it, each including all four nucleoside triphosphates plus DNA polymerase I. At least one of the nucleoside triphosphates is radioactively labeled, usually with 32P. This label allows us to identify newly synthesized DNA by autoradiography. To each of the four subsamples, one of the dideoxynucleotides (dd) is added one subsample gets ddTTP, one gets ddATP, one gets ddCTP, and one gets ddGTP. These dideoxynucleotides are added in addition to the regular deoxynucleotides to increase the probabil-
Add DNA polymerase I plus four deoxynucleotides (dTTP, dATP, dCTP, dGTP), one of which is radioactive, and subdivide into four subsamples
Figure 13.32 Initial steps in the dideoxy method of DNA sequencing. The asterisks indicate the dideoxynucleotides. The
DNA to be sequenced is placed into a primer con guration (a, b). Four reaction mixtures are created, each with all four normal nucleotides plus one of the dideoxynucleotides. Thus DNA synthesis in each reaction mixture is stopped a percentage of the time when the complement to the dideoxynucleotide appears in the template (c).
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