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Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002.

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Biochemistry. 5th edition.

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Section 27.6Mutations Involve Changes in the Base Sequence of DNA

We now turn from DNA replication to DNA mutations and repair. Several types of mutations are known: (1) the substitution of one base pair for another, (2) the deletion of one or more base pairs, and (3) the insertion of one or more base pairs. The spontaneous mutation rate of T4 phage is about 10-7 per base per replication. E. coli and Drosophila melanogaster have much lower mutation rates, of the order of 10-10.

Image ch27fu4.jpg

The substitution of one base pair for another is the a common type of mutation. Two types of substitutions are possible. A transition is the replacement of one purine by the other or that of one pyrimidine by the other. In contrast, a transversion is the replacement of a purine by a pyrimidine or that of a pyrimidine by a purine.

Watson and Crick suggested a mechanism for the spontaneous occurrence of transitions in a classic paper on the DNA double helix. They noted that some of the hydrogen atoms on each of the four bases can change their location to produce a tautomer. An amino group (-NH2) can tautomerize to an imino form (═NH). Likewise, a keto group (

Image ch27fu5.jpg
can tautomerizeto an enol form
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. The fraction of each type of base in the formof these imino and enol tautomers is about10-4. These transient tautomers

can form nonstandard base pairs that fit into a double helix. For example, the imino tautomer of adenine can pair with cytosine (Figure 27.41). This A*-C pairing (the asterisk denotes the imino tautomer) would allow C to become incorporated into a growing DNA strand where T was expected, and it would lead to a mutation if left uncorrected. In the next round of replication, A* will probably retautomerize to the standard form, which pairs as usual with thymine, but the cytosine residue will pair with guanine. Hence, one of the daughter DNA molecules will contain a G-C base pair in place of the normal A-T base pair.


The interconversion of two isomers that differ only in the position of protons (and, often, double bonds).

Figure 27.41. Base Pair with Mutagenic Tautomer.

Figure 27.41

Base Pair with Mutagenic Tautomer. The bases of DNA can exist in rare tautomeric forms. The imino tautomer of adenine can pair with cytosine, eventually leading to a transition from A-T to G-C.

27.6.1. Some Chemical Mutagens Are Quite Specific

Base analogs such as 5-bromouracil and 2-aminopurine can be incorporated into DNA and are even more likely than normal nucleic acid bases to form transient tautomers that lead to transition mutations. 5-Bromouracil, an analog of thymine, normally pairs with adenine. However, the proportion of 5-bromouracil in the enol tautomer is higher than that of thymine because the bromine atom is more electronegative than is a methyl group on the C-5 atom. Thus, the incorporation of 5-bromouracil is especially likely to cause altered base-pairing in a subsequent round of DNA replication (Figure 27.42).

Figure 27.42. Base Pair with 5-Bromouracil.

Figure 27.42

Base Pair with 5-Bromouracil. This analog of thymine has a higher tendency to form an enol tautomer than does thymine itself. The pairing of the enol tautomer of 5-bromouracil with guanine will lead to a transition from T-A to C-G.

Other mutagens act by chemically modifying the bases of DNA. For example, nitrous acid (HNO2) reacts with bases that contain amino groups. Adenine is oxidatively deaminated to hypoxanthine, cytosine to uracil, and guanine to xanthine. Hypoxanthine pairs with cytosine rather than with thymine (Figure 27.43). Uracil pairs with adenine rather than with guanine. Xanthine, like guanine, pairs with cytosine. Consequently, nitrous acid causes A-TG-C transitions.

Figure 27.43. Chemical Mutagenesis.

Figure 27.43

Chemical Mutagenesis. Treatment of DNA with nitrous acid results in the conversion of adenine into hypoxanthine. Hypoxanthine pairs with cytosine, inducing a transition from A-T to G-C.

A different kind of mutation is produced by flat aromatic molecules such as the acridines (Figure 27.44). These compounds intercalate in DNA—that is, they slip in between adjacent base pairs in the DNA double helix. Consequently, they lead to the insertion or deletion of one or more base pairs. The effect of such mutations is to alter the reading frame in translation, unless an integral multiple of three base pairs is inserted or deleted. In fact, the analysis of such mutants contributed greatly to the revelation of the triplet nature of the genetic code.

Figure 27.44. Acridines.

Figure 27.44

Acridines. Acridine dyes induce frameshift mutations by intercalating into the DNA, leading to the incorporation of an additional base on the opposite strand.

Some compounds are converted into highly active mutagens through the action of enzymes that normally play a role in detoxification. A striking example is aflatoxin B1, a compound produced by molds that grows on peanuts and other foods. A cytochrome P450 enzyme (Section 26.4.3) converts this compound into a highly reactive epoxide (Figure 27.45). This agent reacts with the N-7 atom of guanosine to form an adduct that frequently leads to a G-C-to-T-A transversion.

Figure 27.45. Aflatoxin Reaction.

Figure 27.45

Aflatoxin Reaction. The compound, produced by molds that grow on peanuts, is activated by cytochrome P450 to form a highly reactive species that modifies bases such as guanine in DNA, leading to mutations.

27.6.2. Ultraviolet Light Produces Pyrimidine Dimers

The ultraviolet component of sunlight is a ubiquitous DNA-damaging agent. Its major effect is to covalently link adjacent pyrimidine residues along a DNA strand (Figure 27.46). Such a pyrimidine dimer cannot fit into a double helix, and so replication and gene expression are blocked until the lesion is removed.

Figure 27.46. Cross-Linked Dimer of Two Thymine Bases.

Figure 27.46

Cross-Linked Dimer of Two Thymine Bases. Ultraviolet light induces cross-links between adjacent pyrimidines along one strand of DNA.

27.6.3. A Variety of DNA-Repair Pathways Are Utilized

The maintenance of the integrity of the genetic message is key to life. Consequently, all cells possess mechanisms to repair damaged DNA. Three types of repair pathways are direct repair, base-excision repair, and nucleotide-excision repair (Figure 27.47).

Figure 27.47. Repair Pathways.

Figure 27.47

Repair Pathways. Three different pathways are used to repair damaged regions in DNA. In base-excision repair, the damaged base is removed and replaced. In direct repair, the damaged region is corrected in place. In nucleotide-excision repair, a stretch (more...)

An example of direct repair is the photochemical cleavage of pyrimidine dimers. Nearly all cells contain a photoreactivating enzyme called DNA photolyase. The E. coli enzyme, a 35-kd protein that contains bound N5,N10-methenyltetrahydrofolate and flavin adenine dinucleotide cofactors, binds to the distorted region of DNA. The enzyme uses light energy—specifically, the absorption of a photon by the N5,N10-methenyltetrahydrofolate coenzyme—to form an excited state that cleaves the dimer into its original bases.

The excision of modified bases such as 3-methyladenine by the E. coli enzyme AlkA is an example of base-excision repair. The binding of this enzyme to damaged DNA flips the affected base out of the DNA double helix and into the active site of the enzyme (Figure 27.48). Base flipping also occurs in the enzymatic addition of methyl groups to DNA bases (Section 24.2.7). The enzyme then acts as a glycosylase, cleaving the glycosidic bond to release the damaged base. At this stage, the DNA backbone is intact, but a base is missing. This hole is called an AP site because it is apurinic (devoid of A or G) or apyrimidinic (devoid of C or T). An AP endonuclease recognizes this defect and nicks the backbone adjacent to the missing base. Deoxyribose phosphodiesterase excises the residual deoxyribose phosphate unit, and DNA polymerase I inserts an undamaged nucleotide, as dictated by the base on the undamaged complementary strand. Finally, the repaired strand is sealed by DNA ligase.

Figure 27.48. Structure of DNA-Repair Enzyme.

Figure 27.48

Structure of DNA-Repair Enzyme. Image mouse.jpg A complex between the DNA-repair enzyme AlkA and an analog of an apurinic site. Note that the damaged base is flipped out of the DNA double helix into the active site of the enzyme for excision.

One of the best-understood examples of nucleotide-excision repair is the excision of a pyrimidine dimer. Three enzymatic activities are essential for this repair process in E. coli (Figure 27.49). First, an enzyme complex consisting of the proteins encoded by the uvrABC genes detects the distortion produced by the pyrimidine dimer. A specific uvrABC enzyme then cuts the damaged DNA strand at two sites, 8 nucleotides away from the dimer on the 5′ side and 4 nucleotides away on the 3′ side. The 12-residue oligonucleotide excised by this highly specific excinuclease (from the Latin exci,“to cut out”) then diffuses away. DNA polymerase I enters the gap to carry out repair synthesis. The 3′ end of the nicked strand is the primer, and the intact complementary strand is the template. Finally, the 3′ end of the newly synthesized stretch of DNA and the original part of the DNA chain are joined by DNA ligase.

Figure 27.49. Excision Repair.

Figure 27.49

Excision Repair. Repair of a region of DNA containing a thymine dimer by the sequential action of a specific excinuclease, a DNA polymerase, and a DNA ligase. The thymine dimer is shown in blue, and the new region of DNA is in red. [After P. C. Hanawalt. (more...)

27.6.4. The Presence of Thymine Instead of Uracil in DNA Permits the Repair of Deaminated Cytosine

The presence in DNA of thymine rather than uracil was an enigma for many years. Both bases pair with adenine. The only difference between them is a methyl group in thymine in place of the C-5 hydrogen atom in uracil. Why is a methylated base employed in DNA and not in RNA? The existence of an active repair system to correct the deamination of cytosine provides a convincing solution to this puzzle.

Cytosine in DNA spontaneously deaminates at a perceptible rate to form uracil. The deamination of cytosine is potentially mutagenic because uracil pairs with adenine, and so one of the daughter strands will contain an U-A base pair rather than the original C-G base pair (Figure 27.50). This mutation is prevented by a repair system that recognizes uracil to be foreign to DNA. This enzyme, uracil DNA glycosylase, is homologous to AlkA. The enzyme hydrolyzes the glycosidic bond between the uracil and deoxyribose moieties but does not attack thymine-containing nucleotides. The AP site generated is repaired to reinsert cytosine. Thus, the methyl group on thymine is a tag that distinguishes thymine from deaminated cytosine. If thymine were not used in DNA, uracil correctly in place would be indistinguishable from uracil formed by deamination. The defect would persist unnoticed, and so a C-G base pair would necessarily be mutated to U-A in one of the daughter DNA molecules. This mutation is prevented by a repair system that searches for uracil and leaves thymine alone. Thymine is used instead of uracil in DNA to enhance the fidelity of the genetic message. In contrast, RNA is not repaired, and so uracil is used in RNA because it is a less-expensive building block.

Figure 27.50. Uracil Repair.

Figure 27.50

Uracil Repair. Uracil bases in DNA, formed by the deamination of cytosine, are excised and replaced by cytosine.

27.6.5. Many Cancers Are Caused by Defective Repair of DNA

Image caduceus.jpg As discussed in Chapter 15, cancers are caused by mutations in genes associated with growth control. Defects in DNA-repair systems are expected to increase the overall frequency of mutations and, hence, the likelihood of a cancer-causing mutation. Xeroderma pigmentosum, a rare human skin disease, is genetically transmitted as an autosomal recessive trait. The skin in an affected homozygote is extremely sensitive to sunlight or ultraviolet light. In infancy, severe changes in the skin become evident and worsen with time. The skin becomes dry, and there is a marked atrophy of the dermis. Keratoses appear, the eyelids become scarred, and the cornea ulcerates. Skin cancer usually develops at several sites. Many patients die before age 30 from metastases of these malignant skin tumors.

Ultraviolet light produces pyrimidine dimers in human DNA, as it does in E. coli DNA. Furthermore, the repair mechanisms are similar. Studies of skin fibroblasts from patients with xeroderma pigmentosum have revealed a biochemical defect in one form of this disease. In normal fibro-blasts, half the pyrimidine dimers produced by ultraviolet radiation are excised in less than 24 hours. In contrast, almost no dimers are excised in this time interval in fibroblasts derived from patients with xeroderma pigmentosum. The results of these studies show that xeroderma pigmentosum can be produced by a defect in the excinuclease that hydrolyzes the DNA backbone near a pyrimidine dimer. The drastic clinical consequences of this enzymatic defect emphasize the critical importance of DNA-repair processes. The disease can also be caused by mutations in eight other genes for DNA repair, which attests to the complexity of repair processes.

Defects in other repair systems can increase the frequency of other tumors. For example, hereditary nonpolyposis colorectal cancer (HNPCC, or Lynch syndrome) results from defective DNA mismatch repair. HNPCC is not rare—as many as 1 in 200 people will develop this form of cancer. Mutations in two genes, called hMSH2 and hMLH1, account for most cases of this hereditary predisposition to cancer. The striking finding is that these genes encode the human counterparts of MutS and MutL of E. coli. The MutS protein binds to mismatched base pairs (e.g., G-T) in DNA. An MutH protein, together with MutL, participates in cleaving one of the DNA strands in the vicinity of this mismatch to initiate the repair process (Figure 27.51). It seems likely that mutations in hMSH2 and hMLH1 lead to the accumulation of mutations throughout the genome. In time, genes important in controlling cell proliferation become altered, resulting in the onset of cancer.

Figure 27.51. Mismatch Repair.

Figure 27.51

Mismatch Repair. DNA mismatch repair in E. coli is initiated by the interplay of MutS, MutL, and MutH proteins. A G-T mismatch is recognized by MutS. MutH cleaves the backbone in the vicinity of the mismatch. A segment of the DNA strand containing the (more...)

27.6.6. Some Genetic Diseases Are Caused by the Expansion of Repeats of Three Nucleotides

Image caduceus.jpg Some genetic diseases are caused by the presence of DNA sequences that are inherently prone to errors in the course of replication. A particularly important class of such diseases are characterized by the presence of long tandem arrays of repeats of three nucleotides. An example is Hunt-ington disease, an autosomal dominant neurological disorder with a variable age of onset. The mutated gene in this disease expresses a protein called huntingtin, which is expressed in the brain and contains a stretch of consecutive glutamine residues. These glutamine residues are encoded by a tandem array of CAG sequences within the gene. In unaffected persons, this array is between 6 and 31 repeats, whereas, in those with the disease, the array is between 36 and 82 repeats or longer. Moreover, the array tends to become longer from one generation to the next. The consequence is a phenomenon called anticipation: the children of an affected parent tend to show symptoms of the disease at an earlier age than did the parent.

The tendency of these trinucleotide repeats to expand is explained by the formation of alternative structures in DNA replication (Figure 27.52). Part of the array within the daughter strand can loop out without disrupting base-pairing outside this region. DNA polymerase extends this strand through the remainder of the array, leading to an increase in the number of copies of the trinucleotide sequence.

Figure 27.52. Triplet Repeat Expansion.

Figure 27.52

Triplet Repeat Expansion. Sequences containing tandem arrays of repeated triplet sequences can be expanded to include more repeats by the looping out of some of the repeats before replication.

A number of other neurological diseases are characterized by expanding arrays of trinucleotide repeats. How do these long stretches of repeated amino acids cause disease? For huntingtin, it appears that the polyglutamine stretches become increasingly prone to aggregate as their length increases; the additional consequences of such aggregation are still under active investigation.

27.6.7. Many Potential Carcinogens Can Be Detected by Their Mutagenic Action on Bacteria

Many human cancers are caused by exposure to chemicals. These chemical carcinogens usually cause mutations, which suggests that damage to DNA is a fundamental event in the origin of mutations and cancer. It is important to identify these compounds and ascertain their potency so that human exposure to them can be minimized. Bruce Ames devised a simple and sensitive test for detecting chemical mutagens. In the Ames test, a thin layer of agar containing about 109 bacteria of a specially constructed tester strain of Salmonella is placed on a petri dish. These bacteria are unable to grow in the absence of histidine, because a mutation is present in one of the genes for the biosynthesis of this amino acid. The addition of a chemical mutagen to the center of the plate results in many new mutations. A small proportion of them reverse the original mutation, and histidine can be synthesized. These revertants multiply in the absence of an external source of histidine and appear as discrete colonies after the plate has been incubated at 37°C for 2 days (Figure 27.53). For example, 0.5 μg of 2-aminoanthracene gives 11,000 revertant colonies, compared with only 30 spontaneous revertants in its absence. A series of concentrations of a chemical can be readily tested to generate a dose-response curve. These curves are usually linear, which suggests that there is no threshold concentration for mutagenesis.

Figure 27.53. Ames Test.

Figure 27.53

Ames Test. (A) A petri dish containing about 109 Salmonella bacteria that cannot synthesize histidine and (B) a petri dish containing a filter-paper disc with a mutagen, which produces a large number of revertants that can synthesize histidine. After (more...)

Some of the tester strains are responsive to base-pair substitutions, whereas others detect deletions or additions of base pairs (frameshifts). The sensitivity of these specially designed strains has been enhanced by the genetic deletion of their excision-repair systems. Potential mutagens enter the tester strains easily because the lipopolysaccharide barrier that normally coats the surface of Salmonella is incomplete in these strains.

A key feature of this detection system is the inclusion of a mammalian liver homogenate (Section 4.1.2). Recall that some potential carcinogens such as aflatoxin are converted into their active forms by enzyme systems in the liver or other mammalian tissues (Section 27.6.1). Bacteria lack these enzymes, and so the test plate requires a few milligrams of a liver homogenate to activate this group of mutagens.

The Salmonella test is extensively used to help evaluate the mutagenic and carcinogenic risks of a large number of chemicals. This rapid and inexpensive bacterial assay for mutagenicity complements epidemiological surveys and animal tests that are necessarily slower, more laborious, and far more expensive. The Salmonella test for mutagenicity is an outgrowth of studies of gene-protein relations in bacteria. It is a striking example of how fundamental research in molecular biology can lead directly to important advances in public health.

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2002, W. H. Freeman and Company.
Bookshelf ID: NBK22525