Chapter Introduction

DNA Replication, Repair, and Recombination

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Faithful copying is essential to the storage of genetic information. With the precision of a diligent monk copying an illuminated manuscript, a DNA polymerase (above) copies DNA strands, preserving the precise sequence of bases with very few errors.

OUTLINE

  1. DNA Replication Proceeds by the Polymerization of Deoxyribonucleoside Triphosphates Along a Template

  2. DNA Unwinding and Supercoiling Are Controlled by Topoisomerases

  3. DNA Replication Is Highly Coordinated

  4. Many Types of DNA Damage Can Be Repaired

  5. DNA Recombination Plays Important Roles in Replication, Repair, and Other Processes

Perhaps the most exciting aspect of the structure of DNA deduced by Watson and Crick was, as expressed in their words, that the “specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” A double helix separated into two single strands can be replicated because each strand serves as a template on which its complementary strand can be assembled (Figure 28.1). To preserve the information encoded in DNA through many cell divisions, copying of the genetic information must be extremely faithful. To replicate the human genome without mistakes, an error rate of less than 1 bp per 6 × 109 bp must be achieved. Such remarkable accuracy is achieved through a multilayered system of accurate DNA synthesis (which has an error rate of 1 per 103−104 bases inserted), proofreading during DNA synthesis (which reduces that error rate to approximately 1 per 106−107 bp), and postreplication mismatch repair (which reduces the error rate to approximately 1 per 109−1010 bp).

Figure 28.1: DNA replication. Each strand of one double helix (shown in blue) acts as a template for the synthesis of a new complementary strand (shown in red).
Figure 28.3: DNA repair in action. The bacterium Deinococcus radiodurans can reassemble its genome over the course of 3 hours after irradiation with gamma rays to fragment the genome into many pieces. To aid analysis, the genomic DNA samples were digested with a restriction enzyme that cuts at only a few sites within the genome.

Even after DNA has been initially replicated, the genome is still not safe. Although DNA is remarkably robust, ultraviolet light as well as a range of chemical species can damage DNA, introducing changes in the DNA sequence (mutations) or lesions that can block further DNA replication (Figure 28.2). All organisms contain DNA-repair systems that detect DNA damage and act to preserve the original sequence. Mutations in genes that encode components of DNA-repair systems are key factors in the development of cancer. Among the most potentially devastating types of DNA damage are double-stranded breaks in DNA. With both strands of the double helix broken in a local region, neither strand is intact to act as a template for future DNA synthesis. A mechanism used to repair such lesions relies on DNA recombination—that is, the reassortment of DNA sequences present on two different double helices. In addition to its role in DNA repair, recombination is crucial for the generation of genetic diversity in meiosis. Recombination is also the key to generating a highly diverse repertoire of genes for key molecules in the immune system (Chapter 34).

Figure 28.2: DNA Replication, damage, and repair. Some errors (shown as a black dot) may arise in the replication processes. Additional defects (shown in yellow), including modified bases, cross-links, and single- and double-strand breaks, are introduced into DNA by subsequent DNA-damaging reactions. Many of the errors are detected and subsequently repaired.

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The bacterium Deinococcus radiodurans illustrates the extraordinary power of DNA repair systems. This bacterium was discovered in 1956 when scientists were studying the use of high doses of gamma radiation to sterilize canned meat. In some cases, the meat still spoiled due to the growth of a bacterial species that withstood doses of gamma radiation more than 1000 times larger than those that would kill a human being. Each D. radiodurans cell contains between 4 and 10 copies of its genome. Even when these bacterial chromosomes are broken into many fragments by the ionizing radiation, they can reassemble and recombine to regenerate the intact genome with essentially no loss of information (Figure 28.3). These cells can also survive extreme desiccation, that is, drying out, much better than other organisms. This ability is believed to be the selective advantage that favored the evolution of this and related species.