DNA repair mechanism - Both prokaryotic and eukaryotic cells have a number of enzyme-based repair system that deal with damage to DNA. If the repair system cannot correct all the lesions, the result is a mutant cell or if too many mutations remain, death of the cell. Life as we know, it results from a delicate balance between accuracy in the transmission of DNA to daughter cells and progeny organisms and the occasional mutation that affords raw material for evolution. DNA repair systems provide that delicate balance. Selected repair systems are described in this ppt.

1. DNA Repair Mechanism

7. Photoreactivation repair
• Thymine dimers and alkylated bases are often directly
repaired
• Pyrimidine dimers can be directly repaired by a
Photoreactivating enzyme called Photolyase.This enzyme uses
energy from the visible lidht to break the bonds holding the
two Pyrimidines together.
• This enzyme detects and binds to the UV – damaged DNA
site.Then the enzyme absorbs visible light,which activates it so
it can break the bonds holding the Pyrimidines dimers together.
• This restores the Pyrimidines to their original independent
state.
• Finally the enzyme dissociates from the DNA ,the damage is
repaired.

8. Photoreactivation repair
• Damage caused by alkylation is repaired directly.
• After DNA is methylated (or) ethylated ,an enzyme called
methyl guanine methyl transfrease (or) alkyl transferase
comes to the scene to repair the damage.
• It does this by accepting the methyl (or) ethyl group by
itself, thus inactivating the enzyme.
• So we call it as ‘SUICIDE ENZYME’ because it dies
after performing its function.Methyl or Ethyl group added to
the O – 6 position of Guanine can be removed by this enzyme.
• The repair process is therefore expensive,each repair event
costs one protein molecule.

11. Post Replication repair (or) Mismatch repair
system
• Despite the accuracy of DNA polymerase action & continual
proofreading errors still are made during DNA replication.
Remaining mismatched bases & other errors are usually
detected and repaired by Mismatch repair system
• The mismatch correction enzyme scans the newly replicated
DNA for mismatched pairs & removes a stretch of newly
replicated DNA around the mismatch.
• A DNA polymerases then replaces the excised nucleotides &
the resulting nick is sealed with a a ligase.
• Successful postreplication repair depends on the ability of
enzymes to distinguish between Old & Newly replicated
DNA strands.

12. Post Replication repair (or) Mismatch repair system
• This is possible because newly replicated DNA strands lack
methyl groups on their bases,where as older DNA has
methyl groups on their bases of both strands.
• This repair process must occur fairly soon after the mismatch
is created (or) both strands will be methylated and no
distinction between them will be possible.

14. Recombination repair (or)Post
replication repair.
• Recombination repair requires DNA replication before it can
operate,it is also called Post replication repair.
• The DNA must be relicated.It creates a problem for DNA with
pyrimidine dimers because the dimers stop the replication
machinary.
• After a pause, replication continues leaving a gap across from
the dimers(A new primer is required to restart DNA synthesis).
• Next,recombination occurs between the gapping strand &
its homologous on the other daughter DNA duplex.
• This recombination depends on the recA gene product,which
exchanges the homologous DNA strands.

15. Recombination repair
• The net effect of this recombination is to fill in the gap across
from the pyrimidine dimers but create a new gap in the other
DNA duplex.
• However,since the other duplex has no dimer, the gap can
easily be filled in by DNA polymerase & Ligase.
• Note that the DNA damage still exists,but the cell has atleast
managed to replicate its DNA.
• Soon or later, true DNA repair could presumably occur.

18. Excision repair
• 1)Using DNA Glycosylase:
• Certain mutations are recognized by an enzyme called DNA
Glycosylase,which breaks the glycosidic bond between the
damaged base & its sugar.
• This leaves an apurinic (or) a pyrimidinic site (AP
site),which is a sugar without its purine (or)pyrimidine base.
• Once the AP site is created,it is recognized by a 5’ AP
endonuclease that cuts (or)nicks the DNA strand on the 5’ side
of the AP site.(The ENDO in endonuclease means the enzyme
cuts inside a DNA strand,not at the free end.(Greek:Endo -
within)

19. Excision repair
• This step is known as INCISION,creates free ends with in the DNA
strand that signal other enzymes to complete the excision process.
• TWO DIFFERENT PATHWAYS IS POSSIBLE:
• Ist way:
• 5’ — 3’ Exonuclease to start at the nick & move left to right (5’
— 3’),removing nucleotides,including the damaged once.(Exo
means enzyme must start at a free end & degrade the DNA one
nucleotide at a time) In Greek EXO - outside
• 3’AP Endonuclease simply to cut just after the AP site,releasing the
AP deoxyribose phosphate.
• The gap left in each case is filled in by DNA polymerase I & the
final nick is sealed by DNA ligase.

21. Excision repair
• II Way:
• Pyrimidine dimers can also be removed by a DNA glycosylase
differently when compared to previous one.
• In the Pyrimidine dimer , DNA glycosylase cuts the glycosidic
bond between one thymine & its sugar,creating an AP site &
leaving the dimer still attached to the DNA.
• A 3’AP Endonuclease cuts just downstream from the AP site.
• A 5’AP Endonuclease (or) 3’ — 5’ Exonuclease removes several
nucleotides.
• A 5’ — 3’ Exonuclease removes several nucleotides including
Thymine dimer.
• The gap left is filled in by DNA polymerase I & the final nick is
sealed by DNA ligase.

23. Excision repair
• DNA Incision with out AP sites:
• Repair enzyme endonuclease (or)Uvr ABC Endonuclease
bounds to DNA.
• Endonuclease activity cuts damaged DNA strand –8
nucleotides to 5’side of the dimer & 4 - 5 nucleotides to the
3’ side.
• Damaged segment diffuses away.
• The resulting single stranded gap about 12 nucleotides long is
filled by DNA polymerase I & DNA ligase joins the
fragments.

25. SOS (Save Our Soul)Repair
• SOS response is induced when DNA is damaged or
when replication of DNA stops and single stranded
DNA accumulates. Agents such as UV radiations,
methyl methane sulphonate, as well as chemicals that
damages DNA induces SOS response. Rec A and Lex
A gene are major in SOS response induction.
• It is an error-prone repair system that contributes
significantly to DNA changes observed in a wide
range of species.

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