complex and the excision repair enzymes.^109 For example, 70% of photodimers in an active DHFRgene in
Chinese hamster ovary cells are excised in a 24-h period while only 10–20% of photodimers are removed
from the genome overall. Later studies established that this phenomenon is confined to the transcribed
DNA strand while virtually no repair occurs in the non-transcribed strand.
Selective repair is not confined to cyclobutane dimers; (6-4) photoproducts are also removed preferen-
tially from active genes. On the other hand, it appears that N-methylpurine repair is not coupled to tran-
scription while the situation regarding covalent modification by carcinogens, such as N-AAF (Section 8.6.1),
remains to be clarified.
8.11.8 Post-replication Repair
The repair systems described in the preceding sections maintain the integrity of the genetic message in the
cell as long as repair is rapid and is accurately completed before DNA polymerase attempts to copy the
damaged DNA. What happens if repair is slow or deficient? It appears that when DNA lesions block pro-
gression of the replication fork, a major response is the activation of ‘error-prone repair’, without removing
the lesion. Xeroderma pigmentosum is likely caused by a defect in post-replication repair.
SOS repairis the name given to such enhanced repair (ER), which is induced by a wide variety of types
of DNA damage.^110 This is how it seems to work in bacteria. When the advancing DNA polymerase
reaches a lesion that blocks its further progress, for example T<>T or 3-MeA, a very sizeable gap is left
opposite the lesion before replication starts again. This gap can either be made good by recombination
processes, known as recombination-repair(Section 6.7.2), or by the induction of SOS repair.
The SOS process has been most thoroughly studied in E. coliand is one of the functions of the recA
gene protein.^111 Several recA proteinsidentify and bind to any long, single-stranded stretch of DNA, which
has been formed by the recBCD proteins. RecBCD produces ssDNA using its helicase/nuclease activities.
Through interaction with ATP, recA now becomes activated as a protease towards the lexA protein, which
is known to be a multifunctional repressor in control of several DNA repair enzymes. Among the many
consequences of hydrolysis of lexA are the de-repression of ruvAB and recA genes and a reduction in the
3 → 5 exonuclease proofreading activity of DNA polymerase III. The net result is that pol III operates
with decreased fidelity, not only in its ability to read through regions of damage such as T<>T but also
elsewhere in the cell, and this situation persists until the activation of recA as a protease ends. At this point
SOS repair is rapidly switched off.
The mechanism of repairing these large gaps, which can be over 1000 bases long, is highly variable. In
particular, the specificity of elongation varies with several factors: the type of polymerase, the activity of the
3 –5editing nuclease, and the particular type of DNA lesion. For example, in cases where the base modi-
fication behaves as a non-instructional site, there is a strong tendency for the incorporation of an adenine
residue.^112 This explains why transversion mutations are seen when guanines are modified by aflatoxinor
by acetylaminofluorenederivatives. Even then, further elongation in the gap is dependent on the base-
sequence in the template strand on the 5-side of the lesion. The overall result is that ‘long-patch’repair
seems likely to be idiosyncratic for each type of lesion in each mutable site and, above all, is error-prone.
8.11.9 Bypass Mutagenesis
A single mutation that arises from damage to DNA can be described by a two-step mechanism.
Misincorporationis the inclusion in the daughter strand of a nucleotide different from the Watson–Crick
complement to the original residue(s) in the primer strand. Bypassis the process of continued chain
elongation beyond the mis-inserted base at the site of the lesion.^113 This process has been carefully exam-
ined in E. coli through the insertion of synthetic cyclobutane photodimers into oligomers and their use as
templates for pol I in primer extension reactions in vitroand in phage and bacterial replication.
When pol I arrives at a lesion in the template, chain extension of the primer strand can either be terminated
or retarded. Three types of result have now been observed for bypass replicationbeyond a cyclobutane
332 Chapter 8