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DNA Repair
The human genome contains 3 billion base
pairs .
If we have an error one in a million this mean
we will have 3000 errors during each
replication cycle of the genome.
The genome of a typical mammalian cell
accumulates many thousands of lesions during
a 24-hour period.
However, as a result of DNA repair, fewer than
1 in 1,000 becomes a mutation. DNA is a
relatively stable molecule, but in the absence
of repair systems, the cumulative effect of
many infrequent but damaging reactions
would make life impossible.
After synthesis, the DNA may undergo
some damages during the cell life-span,
but naturally there are certain repair
systems present inside the body that can
provide protections against DNA damages.
The rate of DNA repair is dependent on
many factors, including the cell type, the
age of the cell, and the extracellular
A cell that has accumulated a large amount of DNA
damage, or one that no longer effectively repairs
damage incurred to its DNA, can enter one of three
possible states:
1. an irreversible state of dormancy, known
as senescence ( getting old )
2. cell suicide, also known
as apoptosis or programmed cell death
3. unregulated cell division, which can lead to the
formation of a tumor that is cancerous
• The 2015 Nobel Prize in Chemistry was
awarded to Tomas Lindahl, Paul Modrich,
and Aziz Sancar (Turkish-American in the field
of genetics, was born in Mardin in 1946 ), for
their work on the molecular mechanisms of
DNA repair processes. There are two
types: nucleotide excision repair and base
excision repair
I. Mismatch Repair System during
DNA replication
• 1.Exonucleolytic proofreading of DNA
polymerase usually occurring simultaneously
with DNA replication. In these processes DNA
molecules with single mismatched 3’ OH ends do
not become effective templates because
polymerase cannot extend when 3’ OH is not
base paired. DNA polymerase has a separate
exonuclease catalytic site that removes unpaired
residues at the terminus and replace them by the
correct base pair.
• 2. An alternative DNA mismatch repair is a
system which recognizes and repairs major
insertion, deletion and mis-incorporation of
bases. During DNA synthesis the newly
synthesized (daughter) strand often includes
errors and such defective copy of the
mismatch repair gene could have serious
consequences on human health.
• The mismatch repair system carries out the
following corrections:
Removes replication errors which are not
recognized by the replication machine.
Detects structural changes in the DNA helix.
• The newly synthesized strand is preferentially
nicked to be distinguished from the parental
strand. Next step is the binding of mismatch
proofreading complex at the defective base pair
of the new strand, followed by removal of
segment from this strand to be correctly replaced
using the parental strand as a template.
II. Repair of DNA damage after DNA maturation
Main Causes of DNA damage that occur after DNA
1. Chemical pollutants
2. Radiation
Industrial chemicals such as vinyl chloride or
hydrogen peroxide, and environmental chemicals such
as polycyclic hydrocarbons found in smoke and tar
create a large chemical modifications in DNA leading
to the formation of oxidized bases, alkylated bases
such as methyl bases or conversion of one base into
another type (conversion of cytidine into uridine).
• Thermal disruption at elevated temperature
increases the rate of depurination (loss of purine
bases from the DNA backbone) and single strand
breaks. For example, hydrolytic depurination is
seen in the thermophilic bacteria, which grow in
hot springs above 80 °C.
• The main types of DNA damage caused
by these environmental factors are:
1. base loss
2. base modification
3. strands breakage.
Thymine oxidation
Repair of DNA damages
Despite the exposure of DNA to large damaging
environmental factors each day, very few damages
actually have serious effects on human
chromosomal DNA due to highly efficient repair
mechanisms. An inactivation or loss of functions in
these DNA repair systems may cause errors in
replication and lead to genetic diseases such as :
Fanconi anaemia (FA)
• It is a rare genetic disease. Among those
affected the majority develop cancer, most
often acute myelogenous leukemia, and 90%
develop bone marrow failure (the inability to
produce blood cells) by age 40. About 60–75%
of people have congenital defects,
commonly short stature, abnormalities of the
skin, arms, head, eyes, kidneys, and ears, and
developmental disabilities.
Lynch syndrome (HNPCC or hereditary
nonpolyposis colorectal cancer)
It is an autosomal dominant genetic condition that
has a high risk of colon cancer as well as other cancers
including endometrial cancer (second most
common), ovary, stomach, small intestine,
hepatobiliary tract, upper urinary tract, brain,
and skin. The increased risk for these cancers is due to
inherited mutations that impair DNA mismatch repair.
It is a type of cancer syndrome.
Werner syndrome (WS)
It is also known as "adult progeria", is a
rare, autosomal recessive progeroid syndrome (PS),
which is characterized by the appearance of
premature aging. The median and mean ages of
death are 47–48 and 54 years, respectively. The
main cause of death is cardiovascular disease or
Types of DNA repair systems
Base Excision Repair (BER)
BER is a cellular mechanism that repairs
damaged DNA throughout the cell cycle. It is
primarily responsible for removing small, nonhelix distorting base lesions from the genome.
BER is important for removing damaged bases
that could otherwise cause mutations by
mispairing or lead to breaks in DNA during
replication. The repair system containing the
following system:
1. First, a glycosylase enzyme recognizes a specific
type of incorrect base., which then cleaves the Nglycosyl bond to remove the defective nitrogen
base and generating an apurinicor apyrimidinic
(AP) site. Different DNA glycosylasesrecognize
different types of defective bases.
Each DNA glycosylase is generally specific for one
type of lesion. Uracil DNA glycosylases, for example,
found in most cells, specifically remove from DNA
the uracil that results from spontaneous
deamination of cytosine. Mutant cells that lack this
enzyme have a high rate of G≡ C to A=T mutations.
2. The AP sites generated by glycosylase action
are then recognized by AP endonuclease, which
cleaves the phosphodiester backbone
immediately 5' to the AP site, leaving a 3'-OH
and 5'-deoxyribose-phosphate terminus
(incision step).
3. The 5' deoxyribose phosphate is then
removed by specific exonuclease called DNA
deoxyribo-phosphodiesterase (dRpase),
leaving a nick (gap).
4. The second strand is used as a template to
fill in the gap. This process is carried out by a
DNA polymerase and a DNA ligase.
• UV-B light causes covalent cross-linking between
adjacent thymine bases creating cyclobutane
thymine dimmers. Ionizing radiation such as that
created by radioactive or x-rays causes breaks in
DNA strands. When thymine dimers are present,
the double helix is distorted (bent), as the
thymines are pulled toward each other. Hydrogen
bonding to adenines on the opposite strand is
weakened .The distortion causes a loss of
template information. In addition, it can prevent
the advancing replication fork or inhibiting the
process of RNA transcription.
UV irradiation causes dimerization of adjacent thymine bases
Fig. 10-13, p.252
Oxidation damage ( oxygen radicals in the presence of metal ions such as Fe2+
can destroy sugar rings in DNA, breaking the strand.)
Fig. 10-14, p.252
repair in
Fig. 10-15, p.253
Base –excition repair
Fig. 10-16, p.254
Nucleotide Excision Repair (NER)
The related nucleotide excision repair pathway
repairs bulky helix-distorting lesions
1. Specific endonuclease cleaves damaged DNA
on either side of a lesion thereby producing a
short gap.
2. Highly processive DNA polymerase fills in the
gap and DNA ligase completes the repair
Nucleotide-excision repair
Fig. 10-17, p.254
Recombination can be used to repair infrequent lesions
Thymine dimer excision repair system
A photo-reactivating enzyme system that can
recognizes the thymine dimer and in response to
visible light this enzyme system is stimulated to
cleave the thymine rings. The system contains UV
endonuclease that cleaves the damaged DNA on
either side of the dimer to produce a short gap
(about 100 nucleotides) on a single strand that
can be filled by DNA polymerase using opposite
strand as a template. Then the DNA ligase is used
to complete the repair process.
Xeroderma pigmentosum
It is a rare autosomal recessive genetic disorder of DNA repair in
which the ability to repair damage caused by ultraviolet (UV) light is
Nearly 90% of these individuals develop skin
carcinomas Most XP individuals also suffer from
neurologic disorders including mental retardation.
XP individuals are extremely sensitive to sunlight
(UV light) and are unable to efficiently repair
thymine dimers and other types of DNA damages