DNA Repair and its cause of emergence. Mutation and its types. Various repair mechanisms in living organisms with its distinctive types along with two common examples: Progeria and Multiple Sclerosis(MS).

1. DNA REPAIR
By Sivashish Kashyap
B.Sc. 3rd Year, 5th Semester
Centre For Biotechnology
PIMS-DU
Loni, Maharashtra.

2. Contents :
• Introduction
• Cause of
emergence
• Mutations and its
types
• Repair mechanism
and its types
• Diseases due to
repair defects.
• References

4. Introduction
• DNA repair is a collection of processes by which a
cell identifies and corrects damage to the DNA
molecules that encodes its genome.
• Repair mechanism recruits many enzymes that have
detective(scan) and corrective functions.
• Thousands of random changes occur everyday.
• These changes in the cell maybe caused by –
Heat, metabolic accidents, radiation of various sorts
and exposure to substances in the environment.

5. Contd…
• The basic process of repairing includes-

6. Cause of Emergence:
Mutations
• Heritable changes in the genetic material. They are
inherited changes and provide new genetic variation
that allows organism to evolve.
• 3 major factors that leads to mutation :
The accuracy of DNA replication machinery
The efficiency of mechanism that evolved for repair
of damaged DNA
The degree of exposure to mutagenic agents present
in the environment.

7. Mutations
• It can be classified into:
Spontaneously occurring mutations
Induced mutations
• Spontaneously occurring mutations can be further divided
into:
Transition mutation: Replacement of a purine in one
strand of DNA with the other purine and the replacement
of a pyrimidine in the complementary strand with the other
pyrimidine.
Transversion mutation: Base-pair substitution involving
the replacement of a purine with a pyrimidine and vice
versa.

8. Contd…
Frame-Shift mutation: Point mutation that involves
the addition or deletion of one or a few base pairs
which occurs within the coding region of a gene and
alters the reading frame of all base pair triplets.
• Induced mutations can be further classified into
mutations that is induced by :
Chemicals
Radiations
Transposable genetic elements.

9. • Insertion and deletion mutation can affect all parts of the
genome but are particularly prevalent when the template
DNA contains short repeated sequences, such as those
found in microsatellites.
• This is because repeated sequences can induce
replication slippage, which is a new discovery of
replication defect.
• In replication slippage, the template is either copied twice
or missed out and this results in a new polynucleotide that
has either larger or smaller number.
• It might also be responsible for expanding trinucleotide
repeats and its respective inherited human disease. For
example: Huntington’s disease.

10. DNA Repair and its types
• Repair mechanism keeps the mutations inflicted by DNA
damage at a tolerable rate.
• Most DNA repair studies are carried out using E. coli as
the model organism, most of which resemble vertebrate
repair mechanism.
• Five well- characterized mechanism has been
established:
Light dependant repair
Excision repair
Mismatch repair
Post replication repair
The error prone repair system(SOS Response)

11. Light dependant repair
• Photoreactivation of DNA.
• Only found in bacteria and is carried out by a light
activated enzyme called photolyase.
• DNA’s exposure to UV induces thymine dimers
produced by covalent cross linkages.
• DNA photolyase recognizes and binds to thymine
dimers and uses light energy to cleave the covalent
cross links.
• Blue region of the visible light spectrum is best suited
for photolyase activation.

13. Excision repair
• It involves mainly three enzymes:
Endonuclease or exonuclease
DNA polymerase
DNA ligase
• There are 2 major types of excision repair:
Base excision repair
Nucleotide excision repair

14. Base excision repair
• It involves a battery of enzymes called DNA Glycosylases,
each of which can recognize and hydrolyze specific
altered bases like-
Deaminated C’s, deaminated A’s, different types of
alkylated or oxidized bases, bases with opened rings etc.
• The detection takes place by an enzyme mediated
flipping-out mechanism, in which DNA glycosylases travel
along DNA using base flipping and once the altered base
is detected, an AP site is created which can be recognized
by an enzyme called AP endonuclease, which cuts the
phosphodiester backbone, and the damage is then
removed and repaired.

16. Nucleotide Excision Repair
• It removes large lesions like thymine dimers and bases with bulky
side groups.
• A unique excision nuclease activity produces cuts on either side of the
damaged nucleotide and excises an oligonucleotide containing the
damaged base.
• Nucleotide excision repair in case of E. coli mainly requires three
gene products
uvrA
uvrB
uvrC
• Nucleotide excision repair in human occurs through a pathway similar
to the one in E. coli, but it involves about 4 times as many proteins.
• In humans, the excised oligomer is 24 to 32 nucleotide long rather
than the 12-mer removed in E. coli.

18. Mismatch Repair
• Direct, base and nucleotide excision repair recognizes and
acts upon DNA damage caused by mutagens.
• However, these systems cannot repair mismatches resulting
from errors in replication as these mismatched nucleotides
are not abnormal in any way, it’s simply insertion of A, T, G
and C at the wrong position.
• Thus, mismatch repair system comes into action which
detects absence of base pairing between parent and the
daughter strand.
• Once detected, the repair system excises part of the
daughter polynucleotide and fills in the gap, in a manner
similar to base and nucleotide excision repair.

19. • This system can distinguish between the parent and the daughter
strand in a manner that the daughter strand is undermethylated
compared to the full complement of methyl groups in the parent
strand.
• There is a delay between DNA replication and methylation of
daughter strand and it is during this window of opportunity that the
repair system scans the DNA for mismatches and makes the required
corrections.
• E. coli at least have 3 mismatched repair systems:
Long patch
Short patch
Very short patch
• This system requires mainly 4 proteins:
MutH- It distinguishes between the two strands and cleaves the
phosphodiester bond.
MutS- It recognizes the mismatch.

20. • MutL – It coordinates between the two proteins.
• Helicase II – It detaches the single strand containing the
mismatched bases.

21. Post Replication Repair
• A potentially dangerous type of DNA damage occurs
when both strands of the double helix are broken, leaving
no intact template strand for repair.
• Two systems have developed for repairs:
Nonhomologous end joining: The broken ends are
juxtaposed and rejoined by DNA ligation, generally with
the loss of one or more nucleotide at the site of joining.
Homologous end joining: It is quite complex and exploits
the fact that cells are diploid and contains two copies of
each double helix.
oHere, general recombination mechanism are called into
play.

22. oThis system transfers nucleotide sequence
information from the intact DNA double helix to
the site of the double-strand break in the broken
helix.
oIt requires special recombination proteins that
recognizes areas of DNA sequence matching
between the two chromosome and bring them
together.
oA DNA replication process then uses the
undamaged chromosome as the template for
transferring genetic information to the broken
chromosome, repairing it with no change in the
DNA sequence.

24. Diseases Due to Repair
Defects
• DNA repair defects can cause an increased risk of cancer or an
accelerated aging disease or both.
• Two examples:
Xeroderma Pigmentosum: (XP) is a genetic disorder in which
there is a decreased ability to repair DNA damage such as that
caused by ultraviolet (UV) light. Symptoms may include a
severe sunburn after only a few minutes in the sun, freckling in
sun exposed areas, dry skin and changes in skin pigmentation.
Complications include a high risk of skin cancer, with about half
having skin cancer by age 10 without preventive efforts,
and cataracts.

25. • XP is autosomal recessive, with at least nine
specific mutations able to result in the condition, in
which nucleotide excision repair (NER) enzymes are
mutated, leading to a reduction in or elimination of
NER.
• There are various XP repair genes where mutations
occur, leading to degenerated gene products:
XPA - That assembles the DNA repair proteins.
XPB – That unwinds the damaged DNA double helix.
XPC – That is involved in initial damage recognition.
Other such proteins are XPD, XPE, XPF, XPG etc.

28. Progeria
• A progressive genetic disorder that causes children to
age rapidly.
• The genetic mutation occurs randomly and isn't
inherited.
• Symptoms, such as slow growth, short height, small
face and hair loss, begin to appear in the first year or
two of life.
• Severe cardiovascular complications usually develop by
puberty, resulting in death.
• Hutchinson-Gilford syndrome (HPGS) is an extremely
rare autosomal dominant genetic disorder.

29. • HPGS is caused by mutations that weaken the
structure of the cell nucleus, making normal cell
division difficult. Mutations occurs in a gene that
encodes lamin A.
• Lamin A is required for normal nuclear
morphology and proper organization of
heterochromatins.
• It is related to DNA repair in a way that Lamin A is
also necessary for homologous and non-
homologous end joining repair system.
• This in turn increases DNA damage and
chromosomal aberrations along with altered
expression of numerous DNA repair factors.

30. References
• Molecular Biology of the cell,11th Edition By-
Bruce Alberts, Alexander Johnson, Jullian
Lewis.
• Genomes 4 By-T.A. Brown
• Essentials of Molecular Biology, 4th Edition
By- George M. Malacinski
• Principles of Genetics, 6th Edition by- D.
Peter Snustad, Michael J. Simmons.