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Oxidative Damage of DNA. Oxidative damage results from aerobic metabolism, environmental toxins, activated macrophages, and signaling molecules (NO). Compartmentation limits oxidative DNA damage. Oxidation of Guanine Forms 8-Oxoguanine. The most common mutagenic base lesion is 8-oxoguanine.

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Oxidative Damage of DNA

Oxidative damage results from aerobic metabolism, environmental toxins,

activated macrophages, and signaling molecules (NO)

Compartmentation limits oxidative DNA damage


Oxidation of Guanine Forms 8-Oxoguanine

The most common mutagenic

base lesion is 8-oxoguanine



from Banerjee et al., Nature 434, 612 (2005)


Repair of 8-oxo-G

Replication of the 8-oxoG strand

preferentially mispairs with A

and mimics a normal base pair

and results in a G-to-T transversion

8-oxoguanine DNA glycosylase/

b-lyase (OGG1) removes 8-oxo-G

and creates an AP site

MUTYH removes the A opposite 8-oxoG

from David et al., Nature447, 941 (2007)


MTH1 Prevents Incorporation of Oxidized dNTPs into DNA

Free dNTPs are much more

susceptible to oxidative damage

than bases in duplex DNA

Oxidized precursors are

misincorporated and are mutagenic

from Dominissini and He, Nature508, 191 (2014)

MTH1 removes oxidized

nucleotides from the pool


Inhibition of MTH1 Selectively Kills Cancer Cells

MTH1 is not essential in normal cells

Higher levels of ROS in cancer cells

causes a non-oncogene addiction to MTH1

from Gad et al., Nature 508, 215 (2014)


UV-Irradiation Causes Formation of Thymine Dimers

from Lodish et al., Molecular Cell Biology, 6th ed. Fig 4-38


Nonenzymatic Methylation of DNA

Formation of 600 3-me-A residues/cell/day are caused by S-adenosylmethionine

3-me-A is cytotoxic and is repaired by 3-me-A-DNA glycosylase

7-me-G is the main aberrant base present in DNA and

is repaired by nonenzymatic cleavage of the glycosyl bond


Effect of Chemical Mutagens

Nitrous acid causes deamination of C to U and A to HX

U base pairs with A

HX base pairs with C


Repair Pathways for Altered DNA Bases

from Lindahl and Wood, Science 286, 1897 (1999)


Direct Repair of DNA

Photoreactivation of pyrimidine dimers by photolyase restores the original DNA structure

O6-methylguanine is repaired by removal of methyl group by MGMT

1-methyladenine and 3-methylcytosine are repaired by oxidative demethylation


Base Excision Repair of a G-T Mismatch

BER works primarily on modifications

caused by endogenous agents

At least 8 DNA glcosylases are

present in mammalian cells

DNA glycosylases remove

mismatched or abnormal bases

AP endonuclease cleaves 5’ to AP site

AP lyase cleaves 3’ to AP site

from Lodish et al., Molecular Cell Biology, 6th ed. Fig 4-36


DNA Glycosylases

from Xu et al., Mech.Ageing Dev. 129, 366 (2008)

Each glycosylase has limited substrate specificity, but there is redundancy in damage recognition


Mechanism of hOGG1 Action

from David, Nature434, 569 (2005)

hOGG1 binds nonspecifically to DNA

Contacts with C results in the extrusion of corresponding base in the opposite strand

G is extruded into the G-specific pocket,

but is denied access to the oxoG pocket

oxoG moves out of the G-specific pocket, enters the

oxoG-specific pocket, and excised from the DNA


Nucleotide Excision Repair

Repairs helix-distorting lesions

UV-induced pyrimidine dimers

Bulky adducts

Intrastrand crosslinks

ROS-generated cyclopurines


Global Genome NER – Damage Recognition

Probes for helix distorting lesions

XPC is the damage sensor which finds the

ssDNA gap caused by disrupted pairing

UV-DDB (DDB1 and DDB2) can stimulate XPC

binding by extruding the lesion to create ssDNA

from Marteijn et al., Nature Rev.Mol.Cell Biol. 15, 465 (2014)


Transcription-coupled NER – Damage Recognition

Repairs transcription-blocking lesions

CSB, UVSSA and USP7 interact with Pol II

With CSA, promotes backtracking

of Pol II to expose lesion

from Marteijn et al., Nature Rev.Mol.Cell Biol. 15, 465 (2014)


NER – Lesion Verification

TFIIH complex is recruited to the lesion

XPB and XPD are helicases

with opposite polarity

XPD verifies the existence of lesions

and XPA binds to altered nucleotides

RPA protects the undamaged

strand from nucleases

XPG nuclease binds to the complex

from Marteijn et al., Nature Rev.Mol.Cell Biol. 15, 465 (2014)


NER – Strand Excision

XPF nuclease is recruited by XPA and

directed to the damaged strand by RPA

XPF and XPG excises the lesion

from Marteijn et al., Nature Rev.Mol.Cell Biol. 15, 465 (2014)


NER – Gap Filling and Ligation

PCNA recruits DNA polymerase to fill ss gap

Nick is sealed by DNA ligase

from Marteijn et al., Nature Rev.Mol.Cell Biol. 15, 465 (2014)


Chromatin Dynamics in GG-NER

NER is stimulated by an

open chromatin environment

UV-DDB ubiquitylates core histones

and associates with PARP1 which

PARylates chromatin

Histone acetylation stimulates NER

Chromatin remodelling complexes

displace nucleosomes

from Marteijn et al., Nature Rev.Mol.Cell Biol. 15, 465 (2014)


Clinical Implications of Defective NER

GG-NER is elevated in germ cells to maintain the entire genome to prevent mutagenesis

Defective GG-NER increases cancer predisposition

Xeroderma pigmentosum

TC-NER is elevated in somatic cells to repair expressed genes to prevent cell death

Defective TC-NER causes premature cell death, neurodegeration and accelerates aging

Cockayne Syndrome


Mismatch Repair

Repairs DNA replication errors and insertion-deletion loops

Decreases mutation frequency by 102 - 103

Plays a role in triplet repeat expansion, somatic

hypermutation and class switch recombination


Mismatch repair in E. coli

GATC sequences are methylated by dam methylase

Newly replicated DNA is transiently hemimethylated

MutS recognizes a mismatch or small IDL

MutS bends DNA, recruits MutL

and forms a small dsDNA loop

MutH nicks the unmethylated GATC

Helicase unwinds the nicked DNA

which is degraded past the mismatch

Gap is repaired by Pol III and ligase

from Marra and Schar, Biochem.J. 338, 1 (1998)


Mismatch Repair in Eukaryotes

MutS homologs recognize mismatch

and form a ternary complex with

MulL homologs and the mismatch

PMS2 is a mismatch-activated strand-

specific nuclease, and the break is directed

to the strand contain the preexisting nick

EXO1 excises the mismatch

The gap is filled in by PCNA, Pold and DNA ligase

Defective mismatch repair is the primary

cause of certain types of human cancers

from Hsieh and Yamane, Mech.Ageing Dev. 129, 391 (2008)


Causes of and Responses to ds Breaks

DSBs result from exogenous insults

or normal cellular processes

DSBs result in cell cycle

arrest, cell death, or repair

Repair of DSBs is by

homologous recombination

or nonhomologous end joining

from van Gent et al., Nature Rev.Genet. 2, 196 (2001)


Initiation of Double-stranded Break Repair

MRN complex recognizes

DSB ends and recruits ATM

ATM phosphorylates H2A.X and

recruits MDC1 to spread gH2A.X

TIP60 and UBC13 modify H2A.X

MDC1 recruits RNF8

which ubiquitylates H2A.X

RNF168 forms ubiquitin

conjugates and recruits BRCA1

from van Attikum and Gasser, Trends Cell Biol. 19, 204 (2009)


ATM Mediates the Cell’s Response to DSBs

DSBs activate ATM

ATM phosphorylation of p53,

NBS1 and H2A.X influence cell

cycle progression and DNA repatr

from van Gent et al., Nature Rev.Genet. 2, 196 (2001)


Repair of ds Breaks by Homologous Recombination

ssDNAs with 3’ends are formed and

coated with Rad51, the RecA homolog

Rad51-coated ssDNA invades the

homologous dsDNA in the sister chromatid

The 3’-end is elongated by DNA polymerase,

and base pairs with ss 3-end of the other broken DNA

DNA polymerase and DNA ligase fills in gaps

from Lodish et al., Molecular Cell Biology, 5th ed. Fig 23-31


Role of BRCA2 in Double-stranded Break Repair

BRCA2 mediates binding

of RAD51 to ssDNA

RAD51-ssDNA filaments

mediate invasion of ssDNA

to homologous dsDNA

from Zou, Nature 467, 667 (2010)


Repair of ds Breaks by Nonhomologous End Joining

KU heterodimer recognizes

DSBs and recruits DNA-PK

Mre11 complex tethers ends

together and processes DNA ends

DNA ligase IV and

XRCC4 ligates DNA ends

from van Gent et al., Nature Rev.Genet. 2, 196 (2001)


Translesion DNA Synthesis

Replicative polymerase encounters

DNA damage on template strand

Catalytic site of replicative polymerases

is intolerant of misalignment between

template and incoming nucleotide

Replicative polymerase is replaced by TLS

polymerase which inserts a base opposite lesion

Base pairing is restored beyond

the lesion and replicative polymerase

replaces TLS polymerase

TLS can occur in S or G2

from Sale et al., Nature Rev.Mol.Cell Biol. 13, 141 (2012)


There are Multiple TLS Polymerases

TLS polymerases are recruited by

interactions with the sliding clamp

There are multiple TLS polymerases

TLS polymerases have low

processivity and low fidelity,

and lack 3’-5’ exonucleases

TLS polymerases are

selective for certain lesions

from Sale et al., Nature Rev.Mol.Cell Biol. 13, 141 (2012)

Most mutations caused by DNA lesions

are caused by TLS polymerases


TLS Polymerases Can Be Accurate or Error-prone

Pol k bypasses an abasic site and often causes a -1 frameshift

Pol h bypasses a thymine dimer and inserts AA

Pol i is accurate with dA template and error-prone with dT template

Replicative polymerases insert dC or dA opposite 8-oxo-G, Pol i inserts dC

The likelihood that TLS polymerases are error-prone depends

on the nature of the lesion and the TLS polymerase that is utilized


Somatic Hypermutation of Ig Genes Depends on TLS Polymerases

AID deaminates dC to dU

Uracil DNA glycosylase forms

an abasic site, and REV1

incorporates dC opposite the site

MMR proteins lead to the formation of a

ss gap, PCNA is ubiquitylated, and Pol h

is recruited, generating mutations at A-T

from Sale et al., Nature Rev.Mol.Cell Biol. 13, 141 (2012)