DNA REPAIR:

It is a collection of process by which a cell identifies and corrects damage to DNA molecule
and maintains the integrity of its genetic code.
1. MISMATCH REPAIR:
In E.coli Mut S recognizes base base nucleotide mismatches.
 Mut S acts as mismatch recognition protein
 It also possess ATPase activity
MutS binds to mismatch as a homodimer.
MutL interacts physically with MutS, enhances mismatch recognition and recruits
and activates MutH
MutL also binds as homodimer and possess ATPase activity.
 Mutant MutL lacking ATPase activity but proficient in ATP binding can activate MutH
but cannot stimulate MutH in response to a mismatch.
 ATP hydrolysis by MutL is essential for mediating the activation of MutH by MutS
Upon its recruitment and activation by MutS and MutL in the presence of ATP, MutH
specifically nicks the daughter (methylated strand) at site of mispair.
This strand-specific nick provides the initiation site for mismatch-provoked excision .
DNA Polymerase now synthesizes the missing patch with correct nucleotide
sequences.
DNA ligase then ligates the nicked strand.

 
2. DIRECT/ENZYMATIC REPAIR:
Only a few types of DNA damage are repaired in this way, particularly pyrimidine dimers
resulting from exposure to ultraviolet (UV) light and alkylated guanine residues.
The major type of damage induced by UV light is the formation of pyrimidine dimers, in
which adjacent pyrimidines on the same strand of DNA are joined by the formation of a
cyclobutane ring.
 The formation of such dimers induced by UV light distorts the structure of the DNA
chain and blocks transcription or replication.
One mechanism of repairing UV-induced pyrimidine dimers is direct reversal of the
dimerization reaction using Photolyase enzyme. The process is called
photoreactivation.
This mechanism is common to a variety of prokaryotic and eukaryotic cells, including
E. coli, yeasts, and some species of plants and animals.

 Another form of direct repair deals with damage resulting from the reaction between
alkylating agents and DNA.
A particularly important type of damage is methylation of the O 6 position of G,
because the product, O6-methylguanine, forms complementary base pairs with T
instead of C.
This lesion can be repaired by an enzyme (called O6-methylguanine
methyltransferase) that transfers the methyl group from O6-methylguanine to a
cysteine residue in its active site.
3. BASE-EXCISION
The repair of uracil-containing DNA is a good example of base-excision repair, in
which single damaged bases are recognized and removed from the DNA molecule.
Uracil can arise in DNA by two mechanisms:
(1) Uracil is occasionally incorporated in place of thymine during DNA synthesis,
(2) uracil can be formed in DNA by the deamination of cytosine.
 DNA Glycosylase recognizes a damaged base and cleaves between base and
deoxyribose in backbone.
 An AP endonuclease cleaves phosphodiester backbone near AP site.
 DNA Polymerase I initiate repair synthesis and simultaneously remove damaged
strand by its 5’-3’ endonuclease activity.
 DNA Polymerase is then disassociated.
 Nick is sealed by DNA Ligase.
4. NUCLEOTIDE EXCISION:
 Nucleotide-excision repair is catalyzed by the products of three genes (uvrA, B, and
C).
 The protein UvrA recognizes damaged DNA and recruits UvrB and UvrC to the site of
the lesion.
 UvrB and UvrC then cleave on the 3′ and 5′ sides of the damaged site, respectively,
thus excising an oligonucleotide consisting of 12 or 13 bases.
 The UvrABC complex is frequently called an excinuclease
 The action of a helicase is then required to remove the damage-containing
oligonucleotide from the double-stranded DNA molecule.
 The resulting gap is filled by DNA Polymerase I and sealed by ligase.

5. SOS REPAIR:
Comes into action when DNA damage is beyond repairs and cell would enter
apoptosis.
SOS is not a repair mechanism rather just a pathway for synthesis of DNA repair
enzymes.
SOS response intiates at severe DNA damage by UV radiations
SOS response has operon for SOS genes:
This operon is regulated by two gene proteins:

LEX.A REC.A
Repressor of SOS Inducer of SOS
operon operon
SOS response synthesize enzymes for two major pathways:
1. Nucleotide excision Repair
2. DNA translation synthesis- DNA polymerase V is synthesized

Translation DNA synthesis is more of a survival pathway than a repair pathway

because when cells get numerous lesions all DNA repair mechanism fail, at that time
a specialized DNA Polymerase V comes in and synthesizes DNA by by-passing DNA
lesions.
However, this method incorporates wrong nucleotide more frequently.