The Mutability and Repair of DNA

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The Mutability and Repair of DNA
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Replication errors and their repair
The nature of mutations Point mutation
1. Switch of one base for another
2. insertion or deletion of a nucleotide
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Drastic changes in DNA
Deletion Insertion Rearrangement of chromosome
By insertion of a transposon, or aberrant actions
of recombination Process.
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Some replication errors escape proofreading
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Mismatch repair removes errors escape
proofreading
2. The system must correct the mismatch
accurately.
1. It must scan the genome.
Scan DNA
Distortion in the backbone
MutL activate MutH
Embracing mismatch Inducing a kick in
DNA Conformational change in MutS itself
Nicking is followed by Helicase (UvrD) and one of
exonucleases
(III)
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DNA methylation to recognize the parental strain
Once activated, MutH selectively nicks the
Unmethylated strand.
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Directionality in mismatch repair
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Mismatch repair system in Eukaryotics
MutS
MutL
E. coli
MSH (MutS homolog)
MLH or PMS
Eukaryotics
Hereditary nonpolyposis colorectal
cancer (mutations in human homologes of Muts and
MutL)
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DNA damage
Radiation, chemical mutagens, and spontaneous
damage
spontaneous damage due to hydrolysis and
deamination
Deamination converts adenine to hypoxanthine,
base pair with C Deamination converts Guanine to
xanthine, base with C but only two H bonds
deamination
Base pair with A
depurination
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DNA damage
spontaneous damage to generate natural base
deamination
Methylated Cs are hot spot for spontaneous
mutation in vertebrate DNA
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Damaged by alkylation and oxidation
Alkylation at the oxygen of carbon atom 6 of G
O6-metylguanine, often mispairs with T.
Oxidation of G generates oxoG, it can mispair
with A and C. a GC to TA transversion is one of
the most common mutation in human cancers.
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Gamma radiation and X-rays

• Cause double-strand breaks in the DNA, which are
  difficult to repair.
• Ionizing radiation and agents like bleomycin that
  cause DNA to break are said to be clastogenic
  (p245).

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DNA damage by UV
Thymine dimer
These linked bases are incapable of base-pairing
and cause DNA polymerase to stop.
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Mutations caused by base analogs and
intercalating agents
Base analogs
Thymine analog
Analogs mispair to cause mistakes during
replication
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Mutations caused by intercalating agents
Intercalating agents
flat molecules
Causing addition or deletion of bases during
replication
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Repair of DNA Damage DNA repair system
Excision repair systems the damaged nucleotide
is not repaired but removed from the DNA, the
other undamaged strand serves as a template for
reincorporation of the correct nt by DNA
polymerase Recombination repair both strands are
damaged. Sequence information is retrieved from a
second undamaged copy of the chromosome.
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Direct reversal of DNA damage
photoreactivation
Capture energy from light
breaking covalent bond
To its own cytosine
O6-metylguanine
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Base excision repair
DNA glycosylases are lesion-specific and cells
have multiple DNA glycosylases 1. Uracil
glycosylase 2. Another specific glycosylase is
responsible for removing oxoG
AP apurinic or apyrimidinic
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Base excision repair
If a damaged base is not removed by base excision
before DNA replication a fail-safe system oxoGA
repair
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Nucleotide Excision Repair
Recognizing distortions to the shape of the DNA
(thymine dimer or bulky chemical adduct)
4-5 nt away from 3
UvrA detecting distortion
8 nt away from 5
UvrB melting DNA
In E.coli 4 proteins involved
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Nucleotide Excision Repair
The principles of nucleotide excision repair in
higher cells is much the same as in E. coli but
us moer complicated, involving 25 or more
polypeptides. The UVR proteins are needed to mend
damage from UV light Mutants of uvr genes are
sensitive to UV light, and lack the capacity
to remove T-T or T-C adducts.
In human, xeroderma pigmentosum patients have
mutations in seven genes (XP genes). These XP
proteins are corresponding to proteins involved
in nucleotide excision repair.
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Transcription-coupled repair
Involves recruitment to the stalled RNA
polymerase of nucleotide excision repair
proteins It focuses repair on genes being
actively transcribed. TFIIH unwinds the DNA
template during the initiation of transcription.
Subunits of TFIIH include the DNA helix-opening
proteins XPA and XPD.
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Translesion DNA synthesis although are template
dependent, the synthesis in a manner that is
independent of base pairing
obstacles to progression of the DNA polymerase
(or AP site)
Complex of proteins UmuC and D
(Y-family of DNA polymerase)