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Radiation, chemical mutagens, heat, enzymatic errors, and spontaneous decay constantly damage DNA. For example, it is estimated that several thousand DNA bases are lost each day in every mammalian cell due to spontaneous decay. Some types of DNA damage interfere with
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DNA replication and transcription. In the long evolutionary challenge to minimize mutation, cells have evolved numerous mechanisms to repair damaged or incorrectly replicated DNA. Many enzymes, acting alone or in concert with other enzymes, repair DNA. Repair systems are generally placed in four broad categories: damage reversal, excision repair, double-strand break repair, and
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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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12. DNA: Its Mutation, Repair, and Recombination
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The McGraw Hill Companies, 2001
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DNA: Its Mutation, Repair, and Recombination
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postreplicative repair. Enzymes that process repair steps have been conserved during evolution. That is, enzymes found in E. coli have homologues in yeast, fruit ies, and human beings. However, eukaryotic systems are almost always more complex.
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Damage Reversal
Ultraviolet (UV) light causes linkage, or dimerization, of adjacent pyrimidines in DNA ( g. 12.27). Although cytosine-cytosine and cytosine-thymine dimers are occasionally produced, the principal products of UV irradiation are thymine-thymine dimers. These can be repaired in several different ways. The simplest is to reverse the dimerization process and restore the original unlinked thymines. In E. coli, an enzyme called DNA photolyase, the product of the phr gene (for photoreactivation), binds to dimerized thymines. When light shines on the cell,
the enzyme breaks the dimer bonds with light energy. The enzyme then falls free of the DNA.This enzyme thus reverses the UV-induced dimerization. Another example of an enzyme that performs direct DNA repair is O6mGua DNA methyltransferase, which removes the methyl groups from O6-methylguanine, the major product of DNA-methylating agents (fig. 12.28). Although other repair mechanisms seem to be present in all organisms, photoreactivation is not; it is apparently absent in human beings.
Excision Repair
Excision repair refers to the general mechanism of DNA repair that works by removing the damaged portion of a DNA molecule. Various enzymes can sense damage or distortion in the DNA double helix. During excision repair, bases and nucleotides are removed from the damaged strand. The gap is then patched using complementarity with the remaining strand. We can broadly categorize these systems as base excision repair and nucleotide excision repair, which includes mismatch repair. We will discuss only the major repair pathways; others exist. Presumably, redundancy in repair has been selected for because of the critical need to keep DNA intact and relatively mutation free.
Base Excision Repair
A base can be removed from a nucleotide within DNA in several ways: by direct action of an agent such as radiation, by spontaneous hydrolysis, by an attack of oxygen free radicals, or by DNA glycosylases, enzymes that sense damaged bases and remove them. Currently, at least ve DNA glycosylases are known. For example, uracil-DNA glycosylase, the product of the ung gene in
Figure 12.27 UV-induced dimerization of adjacent thymines in
Figure 12.28 The structure of O6-methylguanine. The red color
DNA. The red lines represent the dimer bonds in the adjacent thymines.
shows the modi cation of guanine, in which the normal con guration is a double-bonded oxygen (keto form).
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
12. DNA: Its Mutation, Repair, and Recombination
The McGraw Hill Companies, 2001
DNA Repair
E. coli, recognizes uracil within DNA and cleaves it out at the base-sugar (glycosidic) bond. The resulting site is called an AP (apurinic-apyrimidinic) site, because of the lack of a purine or pyrimidine at the site (see g. 12.23). An AP endonuclease then senses the minor distortion of the DNA double helix and initiaties excision of the single AP nucleotide in a process known as base excision repair. The AP endonuclease nicks the DNA at the 5 side of the base-free AP site. A DNA polymerase then inserts a nucleotide at the AP site; an exonuclease, lyase, or phosphodiesterase enzyme then removes the base-free nucleotide. (Lyases are enzymes that can break C-C, C-O, and C-N bonds.) DNA ligase then closes the nick ( g. 12.29). The replacement of just one base occurs 80 90% of the time. In the remaining 10 20% of cases, several nucleotides may be removed, depending probably on which DNA polymerase (I or III) first repairs the site (fig. 12.29). In mammals, DNA polymerase performs two roles in base excision repair: It both inserts a new base where the AP site was and also eliminates the AP nucleotide residue by exonuclease activity. One question that concerned scientists was how the glycosylases gain access to the inappropriate or damaged bases within the double helix. Recently, it has been demonstrated that these enzymes remove the inappropriate or damaged bases by rst ipping them out of the interior of the double helix in a process called base ipping. For example, the enzyme in human beings that recognizes 8-oxoguanine in DNA (see fig. 12.19), 8-oxoguanine DNA glycosylase, ips the base out to excise it. Base ipping seems to be a common mechanism in repair enzymes that need access to bases within the double helix ( g. 12.30).
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