DNA bases can be altered, either spontaneously, as is the case with cytosine, which slowly undergoes deamination (the loss of its amino group) to form uracil, or by the action of deaminating or alkylating compounds. For example, nitrous acid, which is formed by the cell from precursors such as the nitrates, deaminates cytosine, adenine (to hypoxanthine), and guanine (to xanthine). Dimethyl sulfate can alkylate (methylate) adenine. Bases can also be lost spontaneously. For example, ~10,000 purine bases are lost this way per cell per day. Lesions involving base alterations or loss can be corrected by base excision repair ([BER], Fig. 30.31).
1.
Abnormal base removal: In BER, abnormal bases, such as uracil, which can occur in DNA by either deamination of cytosine or improper use of dUTP instead of dTTP during DNA synthesis, are recognized by specific DNA glycosylases that hydrolytically cleave them from the deoxyribosephosphate backbone of the strand. This leaves an apyrimidinic site, or apurinic if a purine was removed, both referred to as AP sites.
2.
AP site recognition and repair: Specific AP endonucleases recognize that a base is missing and initiate the process of excision and gap filling by making an endonucleolytic cut just to the 5′-side of the AP site. A deoxyribose phosphate lyase removes the single, base-free, sugar phosphate residue. DNA pol I and DNA ligase complete the repair process.
D. Double-strand break repair
Ionizing radiation, chemotherapeutic agents such as doxorubicin, and oxidative free radicals (see p. 148) can cause double-strand breaks in DNA that can be lethal to the cell. [Note: Such breaks also occur naturally during genetic recombination.] dsDNA breaks cannot be corrected by the previously described strategy of excising the damage on one strand and using the undamaged strand as a template for replacing the missing nucleotide(s). Instead, they are repaired by one of two systems. The first is nonhomologous end joining (NHEJ), in which a group of proteins mediates the recognition, processing, and ligation of the ends of two DNA fragments. However, some DNA is lost in the process. Consequently, NHEJ is error prone and mutagenic. Defects in NHEJ are associated with a predisposition to cancer and immunodeficiency syndromes. The second repair system, homologous recombination (HR), uses the enzymes that normally perform genetic recombination between homologous chromosomes during meiosis. This system is much less error prone (“error-free”) than NHEJ because any DNA that was lost is replaced using homologous DNA as a template. HR occurs in late S and G2 of the cell cycle, whereas NHEJ can occur anytime.
[Note: Mutations to the proteins BRCA1 or BRCA2 (breast cancer 1 or 2), which are involved in HR, increase the risk for developing breast and ovarian cancer.]
VII. CHAPTER SUMMARY