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3 Information: genes and genomes

joined by ligation. This can change the DNA sequence if nucleo tides have been trimmed off the cut ends before they rejoin. The other mechanism, repair by homologous recombination , is more accurate. It uses a second copy of the double-stranded sequence, if one is available (for example, if it has been synthesized by DNA replication), to direct the repair. The details of the end joining and recombination mechanisms are complex and are not described here. Translesion synthesis is a repair mechanism of ‘last resort’ If DNA repair fails, there is a ‘last resort’ mechanism that allows the cell to complete DNA replication by synthesizing a new strand across an unrepaired section. This is a highly error-prone process as the damaged section cannot act as a template. Instead, a spe cialized DNA polymerase selects the nucleotides for incorporation without depending on base pairing with the template strand. In E. coli this is known as the SOS response. In eukaryotes several DNA polymerases that are not used in normal replication are able to carry out this translesion synthesis. Defects in DNA repair cause human diseases Inherited mutations affecting proteins needed for DNA repair cause several genetic diseases that predispose to cancer. For exam ple, xeroderma pigmentosum can be caused by a mutation affect ing any one of seven proteins involved in nucleotide excision repair. Sufferers develop skin cancer because they cannot repair DNA damage caused by sunlight (Figure 3.26).

During replication damaged bases may ‘mispair’, introducing mutations. For example, deamination of cytosine forms uracil, which pairs with adenine at the next round of replication, causing conversion of a C:G base pair to A:T. Thymine dimers, on the other hand, completely block replication as the DNA polymerase cannot get past them. Some DNA-damaging agents attack the sugar–phosphate back bone of the DNA rather than the bases. For instance, X-rays can cause double-stranded breaks in the DNA molecule, a particularly dangerous form of damage that can be lethal to the cell. Cells use several mechanisms to repair DNA As damage to DNA occurs continually and can have seriously detrimental consequences, a variety of repair mechanisms have evolved to deal with damage. DNA repair is a complex topic and here we will only consider it in outline. In general, repair mech anisms that occur in prokaryotes, such as E. coli, also take place in eukaryotes, but by more complex mechanisms involving larger numbers of proteins. The main DNA repair strategies can be classified into: (1) Direct repair, where damaged bases are restored to their normal structure. For example, a methyl group can be removed from an alkylated base. (2) Excision repair, where damaged DNA is removed and resynthe sized, using the remaining normal strand as a template. There are two main excision repair mechanisms: nucleotide exci sion repair (NER), in which enzymes remove and replace a short stretch of the DNA, including the damaged section, and base exci sion repair (BER), in which only the damaged base is removed, creating an AP (apurinic or apyrimidinic) site, like the apurinic site shown in Figure 3.25a. To complete BER, the AP sugar– phosphate is cleaved from the backbone and the gap is filled in by DNA polymerase, which adds a new nucleotide to replace the miss ing one. While NER enzymes recognize distortions in the double helix caused by the lesion, BER depends on enzymes that are spe cific for each form of damaged base. NER is therefore the more versatile of the two mechanisms. In E. coli and other organisms, including plants and some ani mals, thymine dimers can be repaired directly. The abnormal bonds between the two bases are cleaved by an enzyme that is acti vated by visible light, called a photolyase. However, placental mam mals do not have photolyase enzymes and remove thymine dimers using excision repair. Double-strand breaks in DNA pose a serious repair problem Double-strand breaks cannot undergo excision repair because there is no undamaged strand to act as a template for resynthesis. Two mechanisms have evolved to tackle these breaks. In the non homologous end-joining mechanism, the two cut ends are simply

Figure 3.26 Xeroderma pigmentosum (XP) patient wearing a protective visor. People with XP cannot repair lesions in their DNA caused by exposure to sunlight, making them prone to developing multiple skin cancers. Source : Alain Jocard/Stringer, Getty Images.

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