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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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1 Restriction endonuclease produces four fragments 1 2 3 4 Fragments are isolated by electrophoresis and denatured
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Double-stranded circle One of the fragments isolated by electrophoresis joins the complementary region of the single-stranded DNA circle isolated from phage heads 3 5
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5 3 Primer Discard + DNA polymerase DNA circle is treated with original endonuclease and denatured
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New growth Figure 13.35 The genome of phage
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New growth is isolated
X174 lent itself to the dideoxy method (originally, the plus-and-minus method) of DNA sequencing. Because the phage occurs in both the single- and double-stranded forms, it can be manipulated for sequencing. The double-stranded form is fragmented with an endonuclease. One fragment is isolated by electrophoresis and hybridized to the single-stranded form, creating a primer for new DNA synthesis and thus for dideoxy sequencing. Newly synthesized DNA can be isolated by treating it with the same restriction enzyme, which will create the same cut made originally. The newly isolated pieces can then be electrophoresed as in gure 13.34.
and hence the plaques are colorless. (M13 doesn t form true plaques because it doesn t lyse the E. coli cells. It does form turbid sites due to reduced bacterial growth.) An oligonucleotide primer can be synthesized that is complementary to a region of the phage DNA upstream from the cloning sites. Single-stranded phage DNA containing a cloned insert is isolated and hybridized with the synthetic oligonucleotide. This operation creates the primer con guration for dideoxy sequencing of the cloned DNA. Virtually any clonable segment of DNA can be sequenced using this very general method. Theoretically, that segment could be any size. Stepladder gels, however, are effective only up to about four hundred base pairs.To sequence larger regions requires sequencing overlapping segments and reconstituting the sequence by the overlap pattern, similar to the
methods we described for amino acid sequencing (chapter 11, box 11.1). Overlapping segments of DNA are usually obtained by using two or more restriction enzymes. The most recent innovation in DNA sequencing involves using four uorescent dyes, each uorescing at a different wavelength (505, 512, 519, and 526 nm); each of the four dideoxy nucleotides has a different dye attached. After the newly synthesized fragments are isolated, the products from all four reactions are run together in the same lane of a polyacrylamide gel.The gel is then scanned with an argon laser that excites the dye molecules. An instrument records the color of the peaks, reading the sequence directly and automatically ( g. 13.37).This method greatly simpli es sequencing since it is automated. It also alleviates the necessity for radioactive tags.
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
BOX 13.3
omplete sequencing of a DNA genome using Sanger and Coulson s plus-and-minus method (the forerunner to the dideoxy method) was rst accomplished with X174, a virus that contains a singlestranded DNA circle of 5,387 bases within its protein capsule. Once injected into the host, the DNA is replicated to form a double helix that then proceeds in normal viral fashion to replicate itself, manufacture its own coat proteins, lyse the cell, and escape. This virus has nine genes. The virion is a small, twenty-faced polyhedron with a small spike at each of its twelve vertices. This spike attaches X174 to E. coli. The coat accounts for one protein and the spike accounts for two. Thus, three of the virus s nine genes manufacture coat proteins. Figure 1 illustrates the location of the genes in X174, obtained through standard mapping methods. From the information obtained from the sequencing of MS2, an RNA virus, geneticists believed that there should always be a nontranslated sequence between genes, presumably for the purpose of controlling expression of each gene. However, careful perusal of the nucleotide sequence of X174 provided several surprises. First, the ends of three genes overlapped the beginnings of the next genes (A-C, C-D, and D-J); in the rst two cases, the initiation codon is entirely within the end of the previous gene, but read in a different frame of reference. In the sequence ATGA, the ATG is the initiation of the next gene, whereas the TGA is the termination of the previous gene. In the D-J
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