What is DNA repair?

Figure 1 -DNA Repair functions

As a major defense against environmental damage to cells DNA repair is present in all organisms examined including bacteria, yeast, drosophila, fish, amphibians, rodents and humans. DNA repair is involved in processes that minimize cell killling, mutations, replication errors, persistence of DNA damage and genomic instability. Abnormalities in these processes have been implicated in cancer and aging (Figure 1).

Figure 2 - Mammalian DNA Repair Systems

There are several different repair pathways in mammalian cells (Figure 2):

a) single step reactions, a direct reversal by a single enzyme like photolyase or O-6-methyl-DNA-alkyltransferase,

b) single and multi-step base excision mechanisms (i.e., glycosylases) and

c) multi-step reactions with pleiotropic specificities from multiple protein components.

An example of the single step reaction is the direct reversal that can be
accomplished by the bacterial photolyase enzyme: a cyclobutane pyrimidine
dimer is converted into two adjacent pyrimidines, and thereby the lesion is

Another multi-step process is the one seen after mismatch formation, often
a consequence of a replicative error. In E. coli, these mismatch bases are
repaired by a set of enzymes, the MutS, MutL and MutH proteins. The MutS
protein recognizes the lesion, and initiates the assembly of a repair
complex containing all three proteins. The MutH protein incises at a GATC
sequence in the unmethylated strand. Next, a MutS, MutL and MutU dependent
excision step removes a section of DNA containing the GATC site and the
mismatch. The resulting single stranded gap is filled in by DNA polymerase
III. There is currently much interest in what the homologous pathway is in
mammalian cells, and whether there is interaction between it and nucleotide

Simple base modifications such as monofunctional alkylations can be removed
by the base excision repair system whereas more complex, bulky lesions are
dealt with by the nucleotide excision repair pathways.

Recombinational repair has been well characterized in bacteria, but these
processes are not well defined in mammalian cells. When there is no
available intact template for the DNA polymerase to copy, a recombination
must take place. An example of this type of repair is the process involved
in the removal of chemotherapeutically introduced DNA interstrand
crosslinks which are typically introduced after treatment with nitrogen
mustards or cisplatin.

Figure 3 - Nucleotide Excision Repair scheme

The most important DNA repair pathway is nucleotide excision repair
(figure 3) that fixes the majority of bulky lesions in DNA. These lesions
include UV induced photoproducts, and bulky adducts such as those derived
from cisplatin and 4-nitroquinoline oxide. Understanding of the enzymology
was previously based on knowledge from work done in E.coli, but now the
molecular events are being characterized in human cells. Nucleotide
excision repair
involves recognition, incision, degradation,
polymerization, and finally, ligation. The recognition steps involve the
ERCC1, XPA and XPF gene products followed by the interaction with the TFIIH
transcription factor. This factor contains the repair genes XPB and XPD
and thus represents a direct molecular link between DNA repair and
transcription. A dual incision event is accomplished by the ERCC1 and XPG
products, and this is followed by excinuclease activity, polymerization and
ligation. There are a number of recent reviews that discuss this pathway
in detail and compare the pathways in bacteria and mammalian cells .

Nucleotide excision repair pathways differ in different parts of the
mammalian genome: separate pathways operate for the repair of active or
essential genomic regions versus regions that are non coding. The in vitro
cell free extract assays, that have been used with considerable success to
determine aspects of the DNA repair enzymology, are all limited to studying
inactive DNA, and as yet there is no assay for in vitro repair of active
genes in mammalian cells. Several laboratories are working on this
problem, and that approach is necessary for optimal biochemical analysis of
the biochemistry of gene specific DNA repair. There are distinct DNA
repair pathways for the bulk genome (inactive genomic regions) and for
gene specific repair of active genes. Some genes may have preferential
repair and even a strand bias of the repair process, and these need to be
understood. Further, there can be variations within genes as well: certain
codons are repaired better than others.

A few human disorders are characterized by defects in DNA repair. Patients
with xeroderma pigmentosum (XP) have clinical sun sensitivity, extensive
freckle-like lesions on sun exposed skin and an approximate 1000-fold
increase of developing skin cancer (basal cell carcinoma, squamous cell
carcinoma and melanoma). About 20% of the XP patients have progressive
neurologic degeneration. XP cells are hypersensitive to UV- induced cell
killing and cell mutations and have defective DNA repair. There are 7 XP
nucleotide excision repair complementation groups (XP-A to XP-G) plus a
variant form with normal excision repair. The genes that are defective in
XP are involved in the nucleotide excision repair and basal transcription
complexes (see above) (figure 3).

Patients with Cockayne syndrome have sun sensitivity, short stature, and
progressive neurologic degeneration. Unlike XP, Cockayne syndrome is not
associated with cancer. Cultured cells from Cockayne syndrome patients are
hypersensitive to killing by UV and have defective DNA repair of actively
transcribing genes. There are 2 complementatoin groups in Cockayne
syndrome. The genes that are defective in Cockayne syndrome are also
involved in both nucleotide excision repair and transcription however,
their precise function is not yet known.

Patients with trichothiodystrophy (TTD) have photosensitivity, short
stature, mental retardation and sulphur deficient brittle hair. TTD is not
associated with cancer. Cells from TTD patients are hypersensitive to
killing by UV and have defective DNA excision repair. The genes that are
defective in TTD have been found to be in XP complementation group D or in
unique TTD complementation groups. The explanation for the marked
differences in clinical features of patients with mutations in the same

Some recent references for more information:

Bohr, V.A., Wassermann, K., and Kraemer, K.H. DNA Repair Mechanisms, Alfred
Benzon Symposium No. 35
, Copenhagen:Munksgaard, 1993.pp. 1-428.

Cleaver, J. and Kraemer, K.H.: Xeroderma pigmentosum and Cockayne syndrome.
In Scriver, C.R., Beaudet, A.L., Sly, W.S., and Valle, D. (Eds.) The
Metabolic and Molecular Basis of Inherited Disease, Seventh Edition. New
York, McGraw Hill, vol III, pp 4393-4419, 1995.

Friedberg, E.C., Walker, G.C., and Siede, W. DNA repair and mutagenesis,
Washington, D.C.ASM Press, 1995. pp 1-698.

Science 266: December 23, 1994 DNA Repair - Molecule of the Year. This
issue contains a series of review articles on DNA repair. pp1954-1960.

Trends in Biochemical Sciences (TIBS) vol 20 No 10: October 1995 (237).
This issue is entirely devoted to review articles on DNA repair. pp.

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