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Organizing DNA Damage and Repair

April Apperson, UCSD SOM OESS


DNA repair acronyms (this page and next page)
BER = Base excision repair MGMT = Methylguanine methyltransferase NHEJ = Non-homologous end joining
HRR = Homologous recombination repair MMR = Mismatch repair TL Pol Translesion Pol zeta


Categorizing DNA Damage
and correlating damage with its sources and potential DNA Repairs
Damage Sources Repaired by:
Helical distortion due to abnormal H-bonds between bases
Mismatch Spontaneous: misincorporation during DNA Pol synthesis or tautomerized bases MMR
ssDNA loops Spontaneous: DNA Pol slipping on repeated sequences MMR
Deaminated
bases (e.g., dU)
Sponteneous hydrolysis due to cellular water
Nitrates (preservatives in hot dogs, etc.)
BER or MMR
Abnormal single nucleotides due to addition of chemical groups
Oxidized bases
(e.g., T-OH)
Spontaneous oxidation by reactive chemicals created by cellular metabolism
Increased by infection that increases release of oxidizing compounds
BER or MMR
Alkylated bases
(e.g., Me-G)
Spontaneous alkylation by reactive chemicals created by cellular metabolism
Chemotherapeutic alkylating agents strongly damage DNA by alkylation
BER, MMR or MGMT
Cross-linked nucleotides connected by abnormal covalent bonds
Pyrimidine dimers UV radiation creates TT or TC pyrimidine dimers TC-NER or GG-NER
Cisplatin Cisplatin chemotherapy cross-links purines (G) with platinum Recognized by MMR
Broken phosphodiester backbone
ssDNA breaks Ionizing radiation (x-rays, gamma rays) PARP with BER
dsDNA breaks Replication across ssDNA breaks in template DNA strand; ionizing radiation (x-rays, gamma rays)
causing such frequent ssDNA breaks that they break both strands in one region
BRCA with HRR or
NHEJ




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Categorizing DNA Repair
and correlating repairs with their target types of damage, accuracy and basic mechanism
MGMT BER with glycosidases MMR

NER

BER with
PARP
HRR with
BRCA
NHEJ

Translesion Pol

What do the proteins of this repair/synthesis system recognize? (colors in this category correlate with Damage table on p. 1)
Specific damaged nucleotides caused by: Minor* helical
distortions due to:
Major** helical
distortions due to:
DNA breaks:

Replication fork
stalled by major
helical
distortion**
Methylated
G
dU (de-aminated C)
other oxidized, alkylated
or de-aminated bases
Mismatch
ssDNA loop

Pyrimidine dimer
Multiple oxidized or
alkylated nucleotides
ssDNA
breaks
dsDNA
breaks
dsDNA
breaks
Is original damage repaired accurately, repaired inaccurately or not repaired?
Accurate Inaccurate: Not repaired;
Direct repair:
MGMT
removes
Me from G
Excision repair uses nucleases to excise damaged nucleotides (if needed),
complementary strand to direct accurate synthesis by Pol, and ligase to make final bond

Uses sister
chromatid to
direct repair
Trims DNA
ends
deletion
New strand syn-
thesis continues
inaccurately
substitutions
Glycosidase recognizes
damaged base and cuts
glycosidic bond to
release it
AP nuclease cuts sugar
from backbone
Pol replaces nucleotide
Ligase makes final bond
Recognition proteins
bind to distortion
and others scan for
Me
CpG to identify
old strand***;
Nucleases remove
DNA back past
distortion;
Pol replaces DNA
Ligase final bond

Also recognizes
Cisplatin adducts
not minor at all
and initiates cell
apoptosis (so MMR
deficient cells are
Cisplatin resistant)
GG-NER: XP recog-
nition proteins bind
to distortion any-
where in genome
TC-NER: CSA/B
proteins ride with Pol
II and bind distor-
tion that stalls Pol II
For both: nucleases
remove 12 nucleo-
tides containing
distortion
Pol replaces DNA
Ligase final bond
ssDNA
break
recog-
nition
proteins
bind
PARP,
which
recruits
BER
nuclease,
Pol
and
ligase to
repair
break.
dsDNA break
recognition
proteins
recruit BRCA,
which recruits
HRR proteins
that use
recombination
mechanism to
accurately
repair dsDNA
break
NHEJ
recognition
proteins
bind broken
ends,
recruit
nucleases
to trim
them, then
ligate them
Stalled replica-
tion fork can
recruit TL Pol
zeta to continue
new strand
synthesis past
the distortion in
template strand,
but Pol zeta
doesnt proof-
read, so it
introduces
mismatches and
substitution
mutations
*Helical distortions that wont stall a replication fork (DNA Polymerases) or RNA Pol II
**Helical distortions severe enough to stall a replication fork (DNA Polymerases) or RNA Pol II
***MMR is only accurate during S phase before new strand has been methylated; otherwise MMR cant determine which strand has correct base.