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Chapter 24 : Excision Repair and Bypass

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Abstract:

In excision repair, damaged DNA is recognized as altered and the damage is cut out. Two types of excision repair, each with important variations, can be distinguished. The first, base excision repair (BER), uses particular enzymes, the DNA N-glycosylases to sense specific damaged bases. The second, nucleotide excision repair is a multiprotein system which recognizes generalized deformation in the DNA. The clear requirement for the RecA protein is explained by the need to support the strand exchanges required for recombination and for the filling of gaps left by the blockage of DNA synthesis along one strand only at the site of pyrimidine dimer or other lesion. The genome codes for at least five different DNA polymerases. The dynamics of the bypass process involving the different DNA polymerases are described in this chapter. The complete replication system is in place and DNA is being replicated, either by progression of the complex along a chromosome, as usually thought, or, as has been suggested for , by the chromosomal DNA moving through a fixed replication site. has a variety of enzymes which cooperate to detect and remove damage from the DNA. Operation of these mechanisms is dependent on the location of the lesions with respect to DNA growing points. Lesions far from such growing points are detected either by small DNA glycosylases that continually test the DNA for aberrant bases or by the UvrAUvrB protein complex, which detects helix distortions and searches the distorted helix for altered bases.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24

Key Concept Ranking

DNA Synthesis
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Genetic Recombination
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DNA Polymerase III
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Chromosomal DNA
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Figures

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Figure 1

Pyrimidine dimers.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
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Image of Figure 2
Figure 2

Some bases recognized by DNA glycosylases as abnormal.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
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Figure 3

Four methods by which organisms deal with damaged DNA.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
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Figure 4

Model for the nucleotide excision repair of nontranscribed DNA in . Reproduced from reference (copyright 2000) with permission from Elsevier and R. D. Wood.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
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Figure 5

Pathways for DNA repair of a stalled replication fork. Reproduced from reference (copyright 2001 National Academy of Sciences) with permission.

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
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Figure 6

The isomerization step in lesion avoidance ( ).

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
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Tables

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Table 1

Dose of radiation at which 37% of bacteria form colonies

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Generic image for table
Table 2

Glycosylases of

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Generic image for table
Table 3

Increased amounts of transcript following UV irradiation

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24
Generic image for table
Table 4

Proteins that may participate in replication fork reactivation

Citation: Strauss B. 2005. Excision Repair and Bypass, p 431-447. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch24

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