Nucleic Acids in Chemistry and Biology

extent of helical distortion resulting from the lesion. Nucleotide excision repair appears to be the domin-
ant type of repair process in bacteria and possibly also in humans.^105
One of the best understood repair systems of this sort is that from E. coli, whose uvrABC genes have
been cloned and their protein products purified.^106 An endonuclease initiates the process by making a
single-strand incision close to the damaged nucleotide. The uvrA protein (114kDa) is an ATP-dependent
DNA-binding protein that recognises and binds to the DNA photolesion and also to many other types of
bulky base-modification. The uvrB (84kDa) and uvrC (70kDa) proteins can now bind and initiate the
repair process by nicks in the damaged strand which are on either side of the lesion and some 12 bases
apart. The excised nucleotide containing the lesion is now released by uvrD (DNA helicase II) while it is
still bound to the protein complex. That leaves a single-stranded gap, which is filled by DNA polymerase
I, which binds and fills the gap from the 3
-end until it approaches the 5
-terminus. Finally, ligation com-
pletes this short-patch repair (Figure 8.43a).
In humans, over 20 proteins contribute to this NER process to combat the damage resulting from UV
radiation,^107 and deficiencies in this repair are responsible for the usually fatal condition of Xeroderma
pigmentosum.
The DNA repair processes of eukaryotes are coming into focus at a molecular level. The fact that their
DNA is organised into higher-order structures (Section 2.6.2) presumably has implications for their DNA
repair processes, as has already been established for their transcription (Section 6.6) and replication (Section
6.6.4). What is clear is that a large number of loci are involved in the excision repair process for eukary-
otes as compared to prokaryotes, yet the mammalian system is remarkably similar to the bacterial system.

8.11.5 Crosslink Repair

We have already seen that DNA cross-links can result from the alkylating activity of various natural, syn-
thetic and photochemical agents (Sections 8.5, 8.7 and 8.8). Most DNA repair mechanisms rely on the
redundant information inherent in the duplex to remove damaged nucleotides and replace them with nor-
mal ones, using the complementary strand as a template. Interstrand cross-links(ICLs) present a special
case of NER and pose a unique challenge to the DNA repair machinery because both strands are damaged.
The repair of ICLs by mammalian cells appears to involve dual incisions, both 5
to the cross-link in one
of the two strands. The net result is the generation of a 22- to 28-nucleotide-long gap immediately 5
to the
cross-link. This gap may act as a recombinogenic signal to initiate cross-link removal.^108 Several human
genes involved in ICL repair have been identified and studies on their mode of action are advancing.

8.11.6 Base Mismatch Repair

The replication of DNA proceeds with a net error rate of around 1 in 10^10. As polymerases have a
nucleotide incorporation error rate of around 1 in 10^5 , and that is improved by their proofreading activity
to 1:10^7 , a further error-reducing process of 1 in 10^3 must exist. It is provided by base-mismatch repair,

330 Chapter 8

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