Nucleotide excision repair (NER) is a pathway that repairs a broad class of helix-distorting lesions in DNA that disrupt transcription and replication. It involves recognizing the damaged site, unwinding the DNA helix, making dual incisions on both sides of the damage, excising the damaged fragment, and resynthesizing the replacement DNA. NER is a complex process involving at least 28 genes and is important for repairing UV-induced damage and protecting against sunlight-induced DNA damage and cancer. Defects in NER genes can cause diseases like xeroderma pigmentosum, trichothiodystrophy, and Cockayne syndrome.

1. NUCLEOTIDE EXCISION
REPAIR PATHWAY

4. Major DNA repair pathways:
•
Nucleotide excision repair (NER)-- deals with
broad class of helix –distorting lesions that disrupt
transcription and replication
•
Base excision repair (BER)-- deals with small
•
Double-strand break (DSB) repair—Homologous
•
Mismatch repair (MMR)– corrects replication errors,
chemical alterations of bases. Particularly relevant for
preventing mutation.
recombination (HR) and Nonhomologous end-joining
(NHEJ)
and can repair alkylated bases.

6. Excision repair directly replaces damaged DNA and then resynthesizes a replacement stretch for the damaged strand.

7. WHAT IS NER?!
 NUCLEOTIDE
EXCISION REPAIR (NER) is a
versatile repair pathway, involved in the removal of
a variety of bulky DNA lesions such as UV induced
cyclobutane pyrimidine dimers (CPD) and
pyrimidine 6-4 pyrimidone photoproducts (6-4PP).
NER is a complex process in which basically the
following steps can be distinguished:
 recognition of a DNA lesion;
 separation of the double helix at the DNA lesion site;
 single strand incision at both sides of the lesion;
 excision of the lesion-containing single stranded
DNA fragment;
 DNA repair synthesis to replace the gap and
 ligation of the remaining single stranded nick.

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The NER pathway involves at least 28 genes. Three NER
genes are also part of the basal transcription factor,
TFIIH. Mutations in 11 NER genes have been associated
with clinical diseases with at least eight overlapping
phenotypes.
NER is involved in protection against sunlight-induced
DNA damage.
Several of the genes involved in NER also affect somatic
growth and development.
Patients with the rare genetic disorders, xeroderma
pigmentosum (XP), trichothiodystrophy (TTD) and
Cockayne syndrome (CS) have defects in DNA
nucleotide excision repair (NER).

9. 
The clinical features of these patients have some similarities but also have
marked differences. While XP patients have 1000-fold increase in
susceptibility to skin cancer, TTD and CS patients have normal skin cancer
risk. Some patients have short stature and immature sexual development.
TTD patients have sulfur deficient brittle hair. Progressive sensorineural
deafness is an early feature of XP and CS. Many of these clinical diseases
are associated with developmental delay and progressive neurological
degeneration. The main neuropathology of XP is a primary neuronal
degeneration. In contrast, CS and TTD patients have reduced myelination of
the brain. These complex neurological abnormalities are not related to
sunlight exposure but may be caused by developmental defects as well as
faulty repair of DNA damage to neuronal cells induced by oxidative
metabolism or other endogenous processes.

10. Excision Repair Systems in E. coli
 The UVR system makes incisions ~12 bases apart on both sides of damaged
DNA, removes the DNA between them, and re-synthesizes new DNA.
 Excision repair systems vary in their specificity, but share the same
general features. Each system removes impaired or damaged
bases from DNA and then synthesizes a new stretch of DNA to
replace them.
 incision : an endonuclease recognizes the damaged area in the
DNA, and isolates it by cutting the DNA strand on both sides of the
damage.
 excision : a 5’-3’ exonuclease removes a stretch of the damaged
strand.

11. Excision-repair removes and
replaces a stretch of DNA that
includes the damaged base(s).

12. The UVR system operates in
stages in which UVRAB
recognizes damage, UVRBC
nicks the DNA, and UVRD
unwinds the marked region.
(The UVR system of excision
repair includes three genes,
UVRA, B, and C, which code
for the components of a
repair endonuclease. UVRD is
a helicase. In almost all (99%)
of cases, the average length
of replaced DNA is ∼12
nucleotides (short-patch
repair).

13. Excision-Repair Pathways in Mammalian Cells
 Mammalian excision repair is triggered by directly removing a damaged base
from DNA.
 Base removal triggers the removal and replacement of a stretch of
polynucleotides.
 The nature of the base removal reaction determines which of two pathways
for excision repair is activated.
 The polδ/ε pathway replaces a long polynucleotide stretch; the polβ pathway
replaces a short stretch.
 The general principle of excision-repair in mammalian cells is similar
to that of bacteria. The process usually starts in a different way,
however, with the removal of an individual damaged base.
 Enzymes that remove bases from DNA are called glycosylases and
lyases.

15. IN A NUTSHELL!!

16. 1. Damage recognition
2. Local unwinding
3. Strand dual incision
4. Repair synthesis and
strand ligation
5. Repaired DNA

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