dna repair mechanism

Department of Biochemistry, Nobel College, Nepal

Friday, April 8,

2016Rajesh Chaudhary

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Students

Why DNA needs to be repaired?

RNA and proteins can be replaced by the information encoded

in the DNA molecule, but DNA itself can’t be replaced by a new

DNA when gets damaged.

Unrepaired DNA leads to cancer production.

Thus, needs repair.

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MUTATION: A permanent change in the nucleotide base of the DNA is

called “mutation”.

Why DNA needs to be repair?

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Xeroderma pigmentosum

Sickle cell anemia

Consequences of unrepaired DNA

Sickle cell anemia

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How DNA gets damaged?

1. By the external environmental factors.

Example: Ionizing radiations, ultra violet rays of sun,

chemical agents, due to toxicity produced in the body.

2. Gets damaged spontaneously.

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Chemistry of DNA damage is diverse and complex.

Rate of DNA damage: 1 million individual molecular lesion per cell/day.

Error made during DNA replication

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Chemical reactions known to create

serious DNA damage

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Both depurination and deamination doesn’t breaks phosphodiester bond.

During the time it takes to read this sentence 1012 purine bases will be lost from DNA due to

depurination reaction.

Deamination and Depurination

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Deamination reaction

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Cytosine Uracil

In DNA spontaneously deamination is corrected by removal of uracil by uracil-DNA glycosylase,

generating abasic (AP) site. The resulting AP is recognized by AP endonuclease enzyme that breaks

phosphodiester bond in the DNA, permitting the repair of the resulting lesion by replacement with

another cytosine.

What are the changes seen in damaged

DNA?

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Formation of Thymidine dimer, Double stranded break

Xeroderma pigmentosum is the result of thymidine dimer

formation because of sunlight exposure

So, how to repair damaged DNA?

Through excision and repair mechanism.

Excision repair is divided into two major categories:

1. Nucleotide excision and repair

2. Base excision and repair

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Basic DNA repair mechanism

1st. (Excision): Damage is cut by one of the series of nucleases each specialized for a type of DNA damage.

2nd. (Re-synthesis): Original DNA sequence is restored by a repair DNA polymerase.

3rd. (Ligation): DNA ligase seals the nick left in the sugar-phosphate backbone of repaired strand.

(NOTE: Ligation requires ATP as energy source.)

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Nucleotide excision repair

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13 Methyl-directed mismatch repair

1. Identification of mismatch strand.

2. Repair of damaged DNA

Methylation and Mismatch repair

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1 2 3

“Mutation in the protein involved

in mismatch repair is associated

with hereditary nonpolyposis

colorectal cancer (HNCC).”

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Lippincott’s Illustrated Review, 5th. Edition

Repair of damage caused by

ultraviolet (UV) light

1. Recognition and excision

of dimers by UV-specific

endonuclease

2. UV radiation and cancer

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Example of E.Coli DNA

Base excision repair

Bases of DNA can be altered, either spontaneously, as in the case

with cytosine, which slowly undergoes deamination to form uracil, or

by the action of delaminating or alkylating compounds.

Approximately 10,000 purine bases are lost this way per cell per

day.

1. Removal of abnormal bases.

2. Recognition and repair of an AP site.

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Correction of base alterations

Correction of base alteration by base

excision repair

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Damage in DNA is recognized by the glycosylase enzyme.

Repair of double stranded break

Double stranded breaks are caused by the high energy

radiation or oxidative free radicals.

Such breaks occur naturally during gene rearrangements.

It can’t be corrected by any of the above mentioned

strategies.

But, can be repaired either by:

1. Non-homologous end-joining repair.

2. Homologous recombination repair.

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Double stranded DNA repair break20

MutationMutation is a sudden and permanent alteration ofnucleotide sequence of the genome of an organism, virus

or extrachromosomal DNA or genetic elements.

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Chemical modifications of nucleotide if left

unrepaired leads to mutation

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Mutation

Somatic mutation: Occurs in non-reproductive cells and

won’t be passed on to offspring and do not matter for

evolution.

Germ line mutation: occurs in reproductive cells like eggs

and sperm and are called germline mutation and it matters

for evolution.

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Mutation on the control gene

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Types of Mutation

1. Substitution

2. Insertion

3. Deletion

4. Frameshift

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How about “Silent mutation”?

Mismatch repair eliminates replication error

and restores DNA sequence

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DNA mismatch repair corrects 99% of

the replication errors increasing overall

accuracy to one mistake in 109 nucleotide

copied.

Failure to repair damaged DNA have severe

consequences

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Importance of mutationsCreates the diversity in a population, thus some

group of population with a particular mutation

might be immune to some disease.

Example: Immune to malaria

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Summary of DNA repair

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dna repair mechanism

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