Base excision repair, nucleotide excision repair, mismatach repair and double strand break repair

1. DNA Repair Systems
R. C. Gupta
Professor and Head
Department of Biochemistry
National Institute of Medical Sciences
Jaipur, India

2. Normally, replication of DNA is extremely
accurate
The new DNA is an exact copy of the
parent DNA
This accuracy is essential for maintaining
the integrity of the genome

3. Errors in replication of DNA can result in
serious consequences
Errors can be spontaneous, or can be
brought about by external agents like:
Chemotherapeutic agents
Ultraviolet light
Ionizing radiation
Mutagenic chemicals

4. If errors are not corrected, mutations can
result
If a cell accumulates mutations, it can turn
into a cancer cell
Unrepaired errors can also push the cell
into apoptosis

5. All organisms possess repair mechanisms
to correct the errors
DNA polymerases themselves have error-
correcting properties
In addition, there are some specific repair
systems in prokaryotes and eukaryotes

6. The repair systems comprise
elements that:
Detect the defect
Remove the defective portion of DNA
Add correct nucleotide(s) in the gap
Ligate the newly added nucleotide(s)
with pre-existing strand

7. DNA repair systems include:
Mismatch repair system
Base excision repair system
Nucleotide excision repair system
Double strand break repair system

8. This system detects a single mismatched
base on the new strand
It corrects the errors that escaped proof-
reading
Mismatch repair system

9. Mismatch repair system has to:
Recognize the newly
synthesized strand
Scan the strand rapidly

10. GATC is a palindromic sequence present
in DNA
GATC sequences are scattered through-
out the DNA
Adenine is methylated in these sequences

13. GATC sequences act as signposts for
mismatch repair system
The system scans the new strand from
one GATC sequence to the next
Mismatched bases distort the DNA
backbone
The system recognizes these distortions

14. MutS scans the new strand from one
GATC sequence to another
If it finds a mispaired base, it binds to it
Then, MutL binds to MutS
In E.coli, the system is made up of three
proteins − MutS, MutL and MutH

15. MutL and MutS activate the GATC endo-
nuclease activity of MutH
Active MutH nicks the new strand just
upstream of the GATC sequence
It goes on removing nucleotides until the
mispaired nucleotide is removed

17. DNA polymerase III adds the correct
nucleotides in the gap
DNA ligase seals the new oligonucleotide
with the DNA strand

19. Base excision repair system
This system recognizes modified bases
that are not normally found in DNA
Such bases may be formed by
deamination of:
Cytosine to uracil
Adenine to hypoxanthine
Guanine to xanthine

23. When the repair system finds an unusual
base, a DNA glycosylase removes it
There are different DNA glycosylases for
different bases
For example, uracil DNA glycosylase
removes uracil

27. Nucleotide excision repair system
This system corrects
errors such as:
Formation of thymine dimers
Addition of exogenous
chemicals to bases

28. Thymine dimers are formed on exposure
to ultraviolet light
Two adjacent thymine bases on a strand
are bonded together

30. Thymine dimer distorts the helix
The nucleotides in the distorted region are
incapable of base pairing

31. Thymine dimer distorts the helix

32. Thymine dimers are removed in E.coli
by uvr ABC excinuclease
uvr ABC excinuclease consists of uvr A,
uvr B and uvr C
uvr A and uvr B detect the error and
unwind the DNA in the region of the defect

33. uvr B nicks the strand a few bases down-
stream of the defect
uvr C nicks it a few bases upstream
Thus, a short oligonucleotide is excised
DNA polymerase I adds the correct nucleo-
tides followed by ligation by DNA ligase

34. A similar but more elaborate repair system
is present in eukaryotes
An inherited defect can occur in this repair
system
This autosomal recessive defect results in
xeroderma pigmentosum in human beings

35. The damage to DNA caused by ultraviolet
light cannot be repaired in xeroderma
pigmentosum
Skin cells bear the brunt of the disease as
they are exposed to sunlight
The disease results in dry and rough skin,
multiple skin cancers and early death

36. The components of
human nucleotide
excision repair
system are:
XPA
XPB
XPC
XPD
XPE
XPF
XPG

37. A sub-pathway of nucleotide excision
repair is transcription-coupled nucleotide
excision repair
This operates when transcription is
arrested at a distorted site in DNA
Blocked RNA polymerase acts as a signal
for this system

38. The stalled RNA polymerase is moved
back
An oligonucleotide, including the defective
portion, is excised
The remaining steps are same as in
standard nucleotide excision repair

39. Two additional proteins are required in
transcription-coupled nucleotide excision
repair
These are CS-A and CS-B
An inherited defect in either of these
causes Cockayne syndrome

40. Double-strand breaks can be caused in
DNA by ionizing radiation
These breaks are extremely deleterious
They disturb replication, transcription and
translation
Double strand break repair system

41. Double-strand breaks can also result in
chromosomal rearrangements
A number of cancers are caused by
chromosomal rearrangements

42. Double-strand breaks are repaired by
homologous recombination (HR) or non-
homologous end joining (NHEJ)
In HR, a sister or homologous chromo-
some is used as a template for repair
In NHEJ, overhanging pieces of DNA
adjacent to the break are joined

43. Synthesis-dependent strand annealing is
the most important mechanism of HR
Is uses information from a sister or homo-
logous chromosome to repair a double
strand break
Homologous recombination

44. DNA having a double strand break finds a
homologous chromosome
5’ Ends of the broken strands are resected
by an exonuclease
The exposed 3’ ends locate complementary
regions in the homologous chromosome

45. The 3’ ends are extended using the
homologous chromosome as template
After completion of synthesis, the
template strands separate and anneal
The repaired strands also anneal with
each other

47. VDJ joining in B cells is an example of
non-homologous end joining (NHEJ)
Class switching also occurs by NHEJ
NHEJ can also repair double strand
breaks
Non-homologous end joining

48. The proteins required in NHEJ are:
• DNA ligase IV
• Ku 70 and Ku 80
• XRCC4 (X-ray cross-complementing
protein 4)
• XLF (XRCC-like factor)
• DNA-Dependent protein kinasecs
• Artemis

49. NHEJ doesn’t require a homologous
chromosome
It uses short homologous DNA sequences
called microhomologies to repair DNA
The microhomologies are present in the
overhanging ends of double-strand breaks
If the overhangs are fully complementary,
NHEJ repairs the break accurately