DNA Damage and Repair

Author: Shenzhou
Reviewer: Shiye

  The faithful inheritance of DNA is essential to the relative stability of a species. Yet factors inside and outside the body act on DNA continuously, making changes to an organism’s DNA unavoidable. The balance between fidelity and change maintains species stability while providing the basis for evolution and the diversity of life.

  DNA damage takes many forms, including base loss, damage to base structure, pyrimidine-dimer formation, single- and double-strand breaks, and DNA cross-linking.

Damage to Base Structure

  Damage to bases and sugar groups is caused mainly by nitrous-acid-induced base deamination and the oxidative modification of DNA bases, including pyrimidines, by oxidizing agents. Bases containing amino groups can also undergo deamination and thereby be converted into other bases; C, for example, can become U.

  When DNA is heated or its pH changes, the glycosidic bond between a base and ribose can be hydrolyzed, causing the base to be lost or detached.

Base Mismatches

  Base mismatches, as well as the deletion or insertion of segments, can occur during DNA replication. Although the proofreading function of DNA polymerase promptly corrects most mismatches as they arise, a very small number remain, at a mismatch rate of about 10-10. Segment deletions or insertions generally occur in short repeated sequences when the number of copies increases during DNA replication. Huntington’s disease is one such case. Patients carry more copies of CAG in the huntingtin gene than other people: a healthy person has no more than 38 copies, while a patient may have 39 or more.

  The addition of base analogs or base-modifying agents can also change the properties of bases and consequently produce incorrect pairing in a DNA sequence.

DNA Cross-Linking

  Absorption of short-wavelength ultraviolet radiation can cause two adjacent thymine bases on one strand to form a covalently linked thymine dimer, also known as an intrastrand DNA cross-link. Short-wavelength ultraviolet radiation can similarly cause other pyrimidines to form dimers, such as CT or CC dimers. Dimer formation can then bend and kink the DNA, interfering with transcription or replication.

DNA Breaks

  DNA breaks are generally caused by ionizing radiation, though they can also result from damage to the pentose structure or from damaged and detached bases. A single-strand break can usually be repaired quickly with the complementary strand as a template. A double-strand break is far less likely to be repaired and requires recombinational repair, which has a high probability of producing chromosomal aberrations.

  Many factors can induce DNA damage, broadly divided into internal and external factors. The main internal factors are reactive metabolites produced by the body and base mismatches during DNA replication. External factors usually include radiation, viral infection, and toxic chemicals. The two categories are not entirely separate, however, because an external factor often triggers an internal one, which then damages DNA. The outcome of DNA damage depends on both the extent of the damage and the cell’s ability to repair it. Cells also have many DNA-repair pathways, including direct repair, excision repair, recombinational repair, and translesion synthesis, which can address the forms of damage described above. One type of damage is not necessarily repaired through only one pathway, nor does any one pathway participate in the repair of only one kind of DNA damage.

Photoreactivation

  Photoreactivation generally repairs pyrimidine dimers and is also known as their direct repair. Organisms contain an enzyme called DNA photolyase, which recognizes pyrimidine dimers on a DNA strand. When excited by visible light at 400 nm, it separates a dimer into its original monomeric nucleotides.

Excision Repair

  Base excision repair generally depends on DNA glycosylase. The glycosylase recognizes a damaged base in a strand and removes it by hydrolysis, producing an abasic site. At the 5′ end of that site, an AP endonuclease cleaves the phosphodiester bond. The other complementary strand is then used as a template for repair, and DNA ligase finally reconnects the strand at the nick, restoring the DNA’s normal structure.

  Another special mechanism addresses base mismatches. Its central problem is distinguishing the mismatched daughter strand from the parental strand. In bacterial DNA, methylation is an important marker. The parental strand is usually highly methylated, whereas the newly synthesized daughter strand has not yet been methylated. The repair system uses this difference to distinguish them.

  A further form of excision repair deals with alterations to the DNA double helix: nucleotide excision repair. Unlike base excision repair, it does not recognize a particular lesion. Instead, it detects the distortion that the damage causes in the DNA helix, cuts the strand on both sides of the distorted region, and removes the damaged single-stranded nucleotides. Finally, it uses the other strand as a template to synthesize new DNA, fill the gap, and complete the repair.

Recombinational Repair

  Severe DNA damage requires more complex repair; a double-strand break, for example, is an extremely serious lesion. Because no complementary strand is available, the sequence information needed for repair cannot be obtained directly. Double-strand breaks can be repaired by homologous recombination or nonhomologous end joining.

  Homologous recombination repair uses an identical sequence shared by the two DNA duplexes participating in recombination, helping ensure that the newly generated sequence is correct. In Escherichia coli, the RecA protein plays the central role. It recognizes and binds DNA strands, associates with damaged DNA, identifies a sister strand with the same sequence, unwinds it, and aligns it with the damaged DNA. The intact strands then serve as repair templates. Other enzymes resolve the crossover and restore the original structure.

  Nonhomologous end joining is one way mammalian cells repair double-strand DNA breaks. It requires little or no sequence homology, so the repaired DNA may differ from the original. Mammals have enormous genomes, however, so the error may not occur in an essential gene, allowing the damaged cell to survive.

  This process can also be regarded as a form of physiological genetic recombination. One example, mentioned previously, is recombination in the immune system, including rearrangement of the receptor genes of B and T lymphocytes and of immunoglobulin genes.

Translesion DNA Synthesis

  There is one more special response to DNA damage. When the damage is too severe, or replication has already begun, the repair system may be unable to work effectively. The cell can then induce one or more emergency pathways that first replicate past the damaged site and attempt to repair it afterward.

  Defects in DNA-damage repair often cause disease. Xeroderma pigmentosum (XP), for example, results from cells’ inability to perform nucleotide excision repair, which makes epidermal cells exceptionally prone to mutation. Patients are therefore more susceptible than other people to skin cancer, melanoma, and related diseases. Genetic disorders such as Cockayne syndrome and trichothiodystrophy are also caused by problems in genes of the nucleotide excision repair system.

  DNA damage is generally regarded as harmful, but the effects of damage repair are usually considered twofold. On the one hand, it can introduce mutations into DNA and provide a basis for biological evolution. On the other, it may obstruct DNA replication or transcription and, in severe cases, cause cell death.