DNA Repair Mechanisms

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12/19/2016

Though a very strict proof reading system is active during DNA synthesis but still errors including mismatched basepairing or addition of one or more than one extra nucleotides can take place. Moreover, DNA is always subjected to

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environmental factors that cause the insertion or deletion of nucleotides. These factor can include agents which can
either be chemical in nature, for instance, nitrous oxide, or radiation, for example, UV, which can combine two
pyrimidines adjacent to one another in the DNA, and high energy rays, which can lead to double stranded breaks.
Nucleotide bases are also lost from mammalian cells at a rate of several thousand nucleotides per cell per day. If the
damage is not repaired via DNA repair, it can cause a permanent change (mutation) in DNA which can result in many
harmful eects, including failure to control the cell division, leading to cancer. Fortunately, cells are very ecient at
repairing damage caused to their DNA. Major repair systems include recognition of the lesion on the DNA, deletion of
the damaged site, replacement of the gap left by deletion using the complementary strand as a template for DNA
synthesis, and ligation. Therefore, these repair systems carry out excision repair, with excision of one to 10s of bases,
and it reduces the error proportion from one in ten million nucleotides to one in a billion. Four main types of DNA
repair systems are explained below.
1) Methyl-directed Mismatch Repair
Occasionally, errors during DNA replication escape the proof reading activity of DNA polymerase, leading to mismatch
of one to numerous nucleotides. In Escherichia coli, mismatch repair is carried out by a proteins referred to as the Mut
proteins (Fig A). Homologous proteins are found in humans. This repair system proceeds in following steps.
Step I: Identication of the Mismatch Strand
When mismatch occurs during DNA synthesis, the Mut proteins must be capable of dierentiating between correct
strand and the strand containing mismatch. The dierence is based on the degree of methylation. GATC sequences
are found almost every one thousand bases, and these are methylated on adenine residues. This is not carried out
instantly after synthesis, so this makes newly synthesized DNA distinguished as it is hemimethylated i.e., the parent
strand is fully methylated but the daughter strand is not methylated. The methylated parent strand is considered to be
correct and the daughter strand undergoes for repair.

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Figure A: Methyl Directed Mismatch Repair

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Step II: Repair of Damaged DNA

After the identication of strand containing mismatch, an endonuclease incisions the strand and the mismatch is
deleted by an exonuclease. The gap is lled by a DNA polymerase using the complementary strand as a template.
The 3 OH group of newly synthesized DNA is joined with the 5 phosphate of the residual DNA section of the original
DNA by DNA ligase.
2) Repair of Damage caused by Ultraviolet (UV) light
When a cell is exposed to UV, it can result in the joining of two adjacent pyrimidines covalently and lead to the
production of dimers. These dimers inhibit the activity of DNA polymerase by preventing it from replicating the DNA
strand after the position of dimers. Dimers in bacterial genome are removed by uvrABC proteins as explained in g. B.
In humans, similar proteins known as XP proteins are present. This process follows steps mentioned below.
Step I: Recognition and Deletion of Dimers by Ultraviolet-specic Endonuclease:
Initially, an ultraviolet-specic endonuclease (referred to as uvrABC) recognize the dimer, excises the damaged
fragment on both the 5 and 3 side of the dimer and the nucleotide sequence containing the dimer is released, leaving
a gap in the DNA. This gap is lled by same process mentioned above.
UV Radiation and Cancer:
When humans are exposed to unltered sunlight, it can
lead to production of pyrimidine (thiamine) dimers in the
skin cells. In a rare genetic condition known as
Xeroderma pigmentosum (XP), cells are unable to repair
the DNA damage, resulting in a large number mutations
and, subsequently, several skin cancers. This disease is
caused when the genes encoding for nucleotide excision
repair of DNA damage caused by UV in humans are
damaged.

Figure B: Nucleotide Excision Repair of Thiamine Dimers in Escherichia

coli

3) Base Excision Repair

The nucleotide bases of DNA can be changed, either
suddenly, as cytosine does, which slowly loss its amino
group to form uracil, or by reaction with alkylating and
deaminating compounds. For instance, nitrous oxide,
easily removes amino group from cytosine, adenine and
guanine. Nucleotides can also be lost simultaneously.
E.g. at least 10,000 purines are lost via this method per
day.
Step I: Removal of Abnormal Bases:
Abnormal bases, such as uracil which is formed by
deamination of cytosine, are removed from deoxyribosephosphate backbone of the DNA strand by enzymes
called glycosylases. This leaves behind a gap called
apyrimidinic (or apurinic if a purine was deleted), both
called AP site.
Step II: Recognition and Repair of an AP Site:
AP specic endonuclease recognize the missing base
and start the process of deletion and gap lling by
forming an endonucleolytic excision on the 5 side of the
AP site. Subsequently, a deoxyribosephosphate lyase
deletes the single sugar phosphate residues. A DNA

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polymerase and DNA ligase carries out the repair

process.

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Fig C: Base Excision Repair

4) Repair of Double-strand Breaks

High energy rays or free radicals can form double stranded breaks in the DNA, which are possibly lethal to the cell.
Gene rearrangements can also lead to such breaks. Double stranded breaks cannot be repaired by the above
mentioned repair systems. They are corrected by one of two repair systems. First one is nonhomologous end joining
repair which bring together two fragments of DNA by action of a group of proteins. Nevertheless, some DNA is lost in
this process. As a result, this repair mechanism is mutagenic and therefore, it can lead to cancer and
immunodeciency syndromes. The second repair mechanisms, referred to as homologous recombination repair, uses
enzymes which are active during meiosis and carry out recombination between homologous chromosomes. This
mechanism is very much accurate as any lost DNA is replaced by using homologous DNA as a template.

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