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Nucleic Acid Synthesis 867

external agents, including environmental genotoxic com- tion of critical oncogenes and/or tumor suppressor genes,
pounds, drugs, and radiation. Contrary to an earlier belief thus causing uncontrolled cellular multiplication and pre-
that DNA is a rather inert chemical, it is, in fact, sensitive vention of cell death. Prevention of transcription of bulky
to certain chemical reactions, e.g., depurination (loss of adducts in active genes triggers nucleotide excision repair,
purine bases) and deamination of C to U, which occurs at at least in eukaryotes, in a process called “transcription-
a low but significant rate in DNA. It has been estimated coupled repair.” In fact, the repair complex has co-opted
that several hundred to several thousand such lesions are certain proteins of the transcription complex.
generated in the genome of a human cell per day. Both of Although excision repair requires DNA synthesis, it
these changes could be mutagenic. Loss of purines leads is distinct from normal semi-conservative replication be-
to abasic sites in DNA, which could direct misincorpora- cause it occurs throughout the cell cycle and may utilize
tion of wrong bases during DNA replication. Conversion nonreplicative DNA polymerases in both prokaryotes and
of C into U is definitely mutagenic, because the change eukaryotes. Pol II and Pol I in E.coli and DNA polymerase
ofaG•CtoaG•U pair will give rise to one G•C pair β have been identified as such repair polymerases. How-
and one A•T pair after DNA replication because U, like ever, replicative polymerases can also be recruited in some
T, pairs with A. Often, C in the mammalian genome is cases, e.g., for mismatch repair synthesis.
methylated at the C-5 position, as discussed elsewhere, Interestingly, during the last couple of years, a whole
and 5-methyl C is deaminated more readily than C. Its family of DNA polymerase have been identified and char-
conversion to T induces the same G•C → A•T mutation acterized in E. coli, yeast, and mammals (Table II). These
and, unlike deamination of C → U, does not produce an enzymes are unique in their ability to bypass DNA base
“abnormal” base in the DNA. A variety of environmen- adducts which have lost the ability to base pair and thus
tal chemicals and both ultraviolet light present in sun- are not utilized by standard DNA polymerases. It has been
light and ionizing radiation from radioactive sources and suggested that these replication bypass polymerases allow
X-rays induce a plethora of DNA lesions which include cell survival by allowing DNA replication even at the cost
both base damage and sugar damage and are accompanied of introducing mutations.
by DNA strand breaks. Many of these lesions, in partic-
ular, strand breaks and bulky base adducts, are toxic to B. Post-Replication Recombinational Repair
the cells by preventing both replication and transcription.
In contrast to the excision repair process in which the
Other types of base damage and adducts can be mutagenic
DNA damage is actually removed, both eukaryotic and
because they will allow DNA replication to proceed, but
prokaryotic cells have a novel mechanism of adapting to
will direct incorporation of improper bases in the progeny
persistent, unrepaired damage by utilizing homologous
strand.
recombination between the replicated progeny genomes.
Recombination, the process of exchange between homol-
A. Prevention of Toxic and Mutagenic Effects
ogous DNA segments, involves unwinding of one duplex
of DNA Damage by Repair Processes
DNA and reciprocal strand exchange. When one strand
Multiple repair processes have evolved to restore genomic in the parental DNA has a persistent lesion that pre-
integrity in all organisms ranging from bacteria to mam- vents replication, a complete duplex is generated from the
mals. Excision repair comprises one class in which the other, undamaged strand. The new strand subsequently
damaged part of a DNA strand is excised enzymatically acts as the template for the damaged region by strand ex-
fromtheduplexDNA,leavingasingle-strandgap.Thegap change during replication of the damaged strand. Thus,

isthenfilledbyDNApolymerasesstartingatthe3 -OHter- recombination allows synthesis of the correct DNA se-
minus by utilizing the undamaged complementary strand quence opposite the lesion.
as the template, followed by ligation of the nascent seg-

ment to the 5 phosphate terminus at the other end of the
gap with DNA ligase. The excision repair process con- V. DNA MANIPULATIONS AND THEIR
sists of three subgroups which are utilized for distinct
APPLICATIONS
types of damage, although there is some overlap in their
activities. Base excision repair is more commonly used
A. Episomal DNA and Recombinant
for small base adducts, and nucleotide excision repair is
DNA Technology
used for replication/transcription-blocking bulky adducts.
Mismatch repair evolved primarily to remove DNA mi- Extrachromosomal or episomal DNA, present in prokary-
spairs that are generated as errors of replication. Both nu- otes and lower eukaryotes, is distinct from the genome
cleotide excision and mismatch repair deficiencies have of organelles such as mitochondria or chloroplasts and
been linked to tumorigenesis, which results from muta- serves many purposes. In bacteria, plasmid DNA can be