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
recombination (HR) and Nonhomologous end-joining
and can repair alkylated bases.
Excision repair directly replaces damaged DNA and then resynthesizes a replacement stretch for the damaged strand.
WHAT IS NER?!
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 repair synthesis to replace the gap and
ligation of the remaining single stranded nick.
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
NER is involved in protection against sunlight-induced
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).
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.
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
incision : an endonuclease recognizes the damaged area in the
DNA, and isolates it by cutting the DNA strand on both sides of the
excision : a 5’-3’ exonuclease removes a stretch of the damaged
Excision-repair removes and
replaces a stretch of DNA that
includes the damaged base(s).
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
Excision-Repair Pathways in Mammalian Cells
Mammalian excision repair is triggered by directly removing a damaged base
Base removal triggers the removal and replacement of a stretch of
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