DNA Mutations and

Repair

Naina Kalra
Neelam Jamil
Hameeda Arbab
Sehrish Jameel
Department of Microbiology
Faculty of Life Sciences & Informatics (FLSI)
BUITEMS 1
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 Introduction
• A mutation is a change in the nucleotide sequence or gene and can
create new cellular functionalities or lead to the dysfunction of others
• The substances that can induce mutations are known as mutagens
• Cell has got repair mechanisms

05/02/2024 06:45 PM Figure: Mutation in fingers 2

 Mutagens

05/02/2024 06:45 PM Figure: Different mutagens that can cause mutations 3

 Physical mutagens
• UV radiation: Radiation of 260nm induces dimerization of pyrimidine
bases ,purine bases are less common.

• Ionizing radiation:Can cause insertions, deletions, damage to the DNA

• Heat :Stimulates the water induced cleavage of glycosidic bond that

attaches the base to sugar or results in baseless sight leaving gaps in
DNA and making it unstable

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 Chemical mutagens
• Base analogs: Cause point mutations ,these are purines or pyrimidine
bases that are similar enough to be incorporated into nucleotides .the
resulting molecule can then be used as a substrate for DNA synthesis

• 5 bromouracil: Has same base pairing as thymidine

• 2aminoadenine: Analog of adenine

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 Deaminating agents
• Causes point mutation
• Causes removal of amino group from the bases
• Occurs spontaneously but its rate can be increased by
chemicals
• Thymine has no amino group so it cannot be deaminated
• Deamination of adenine gives hypoxanthine which pairs with C
rather than T and deamination of cytosine gives uracil

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 Alkylating agents
• Point mutations
• Ethyl methane sulfonate (EMS)
• Adds alkyl group to nucleotide
• Blocks replication by forming cross links between two strands
of DNA
• Prevents progression of replication fork

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 Intercalating agents
• Insertion mutations
• Best known mutagen is ethidium bromide
• These are small molecules hat can slip between base pairs in
double helix and slightly unwinds it and increases the distance
between adjacent bases

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 The changes reflect in :

Replication

Transcription Translation

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 Types of mutations
1. Point mutation: A point mutation or single base substitution is a type of
mutation that causes the replacement of single base nucleotides with
another nucleotides of DNA

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 Substitution
• Transversion: these are characterized by replacement of a purine by a
pyrimidine or vice versa

• Transitions: in this case a purine or pyrimidine is replaced by another

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 Substitution

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05/02/2024 06:45 PM Figure: Showing sickle cell and a normal red blood cell 16
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 Mutation classification
Mutation may be subtle or severe
• Morphological mutations : affect the outwardly visible properties of an
organism
• curly wings in Drosophila
• dwarf peas

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 Cont…
• Lethal mutations: mutations lead to the death of the individual. Death
does not have to occur immediately, it may take several months or even
years

• Most lethal genes are recessive

• Examples of diseases caused by recessive lethal alleles are cystic fibrosis

and sickle-cell anemia

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 Cont..
• Conditional mutations: a mutant allele causes a mutant phenotype in
only a certain environment called the restrictive condition, but causes
a wild-type phenotype in some different environment, called
the permissive condition

Figure: Showing sesame cat that can change color in

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 Cont…
• Loss of function mutation
• Gain of function mutation

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 If there are problems there must be solutions
to those problems

DNA Repair

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 Direct Repair
Systems fill in nicks
and correct some
types of nucleotide
modification

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 Direct Repair – Nick
Repair
• Nicks can be repaired by a DNA ligase if only a
phosphodiester bond has been broken, without
damage to the 5′-phosphate and 3′-hydroxyl
groups of the nucleotides either side of the nick
• Nicks results from the effects of ionizing radiation

05/02/2024 06:45 PM Figure: Repair of a Nick by DNA Ligase

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Figure source: Wiley-Liss. (2002). Mutation, Repair and Recombination. In B. TA, & 2nd (Ed.), Genomes. Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK21114/
Direct Repair – Alkylation
• Some forms of alkylation damage
are directly reversible by enzymes
that transfer the alkyl group from
the nucleotide to their own
polypeptide chains.
• E.g. Ada enzyme of E. coli -
removes alkyl groups attached to
the oxygen groups at positions 4
and 6 of thymine and guanine

Figure: Direct Reversal Repair of Alkylation Damage

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Direct Repair – Dimers
• Pyrimidine dimers are
repaired by a light-dependent
direct system called
photoreactivation.
• In E. coli, the process involves
the enzyme called DNA
photolyase
• Activated by light with a
wavelength between 300 and
500 nm
Figure: Direct Reversal Repair of Pyrimidine Dimers

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 Excision Repair
• Base Excision Repair
• Nucleotide Excision Repair

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Base Excision Repair (BER)
Variety of DNA glycosylases, for different types of damaged bases.

Various DNA glycosylases recognize lesion and remove base at glycosidic bond,
thereby producing an “abasic” or AP (apurinic/ apyrimidinic) site by base “flipping
out”
One of several AP endonucleases cuts phosphodiesterase backbone adjacent to AP
site

AP nucleotide removed by exonuclease and patch refilled by DNA polymerase and

ligated by DNA ligase

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 Figure Source: Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K.,
and Walter, P. (2002). DNA repair. In Molecular biology of the cell
(4th ed.). New York, NY: Garland Science.

Figure: Base Excision Repair

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Nucleotide Excision Repair (NER)
Used for repair of DNA adducts

Produced by chemical and UV radiation damage

EXAMPLES: thymine-thymine dimers

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NER
Recognizes bulky lesions that block DNA replication (i. e. lesions produced by
carcinogens)--example, UV pyrimidine photodimers
Common distortion in helix

Incision on both sides of lesion

Short patch of DNA excised, repaired by repolymerization and ligation

In E. coli, mediated by UvrABCD

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 Figure source: Wiley-Liss. (2002). Mutation, Repair and Recombination. In B. TA, & 2nd (Ed.),
Genomes. Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK21114/

Figure: Nucleotide excision repair in Escherichia coli.

The damaged nucleotide is shown distorting the helix
because this is thought to be one of the recognition
signals for the UvrABC trimer that initiates the process.

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 Figure Source: Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and
Walter, P. (2002). DNA repair. In Molecular biology of the cell (4th ed.). New
York, NY: Garland Science.

Figure: Nucleotide excision repair

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 Mismatch Repair
When mismatched bases escape
proofreading

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 Mut
Proteins

MutH MutL
MutS
- Binds to unmethylated - Links Mut S and Mut H
Recognizes the mismatch
5′-GATC-3′ sequences
on daughter strand - Activates Mut H
- Cuts the phosphodiester
bond immediately
upstream of the G

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 Double Strand Break
Repair
• Non-homologous end joining
• Homologous end joining - Recombination

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 DSB Repair – Non homologous end join
• Involves two proteins
• Ku protein, a hetero dimer with two subunits bind to free DNA ends & has
latent ATP dependent helicase activity
• DNA dependent Protein kinase ( DNA – PK )

• How the system works?

• DNA – PK phosphorylates Ku resulting in activation of the Ku helicase.
• This results in unwinding of the 2 ends.
• The unwound approximated DNA forms base pairs.
• The extra nucleotide tails are removed by an exonuclease & the gaps are filled
and closed by DNA ligase .
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 DSB Repair – Homologous end join
• In homologous recombination, information from the homologous
chromosome that matches the damaged one (or from a sister
chromatid, if the DNA has been copied) is used to repair the break
• Undamaged region of the homologue or chromatid is used as a
template to replace the damaged region of the broken chromosome.
• Homologous recombination is “cleaner” than non-homologous end
joining and does not usually cause mutations

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 Figure: Homology Directed Repair

Figure Source: Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K.,
and Walter, P. (2002). DNA repair. In Molecular biology of the cell
(4th ed.). New York, NY: Garland Science.

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 Conclusion
• DNA is a highly stable and versatile molecule. Though sometimes the
damage is caused to it, it is able to maintain the integrity of information
contained in it.
• The most frequent sources of damage to DNA are the inaccuracy in DNA
replication and chemical changes in DNA
• DNA has many elaborate mechanisms to repair any damage or distortion.
• A change in the sequence of bases if replicated and passed on to the next
generation becomes permanent and leads to mutation. At the same time
mutations are also necessary which provide raw material for evolution.

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References
• Branze, D., & Foiani, M. Regulation of DNA repair throughout the cell cycle. Nature
Reviews Molecular Cell Biology 9, 297–308 (2008) doi:10.1038/nrm2351.pdf
• Clancy, S. (2008). DNA damage & repair: mechanisms for maintaining DNA integrity.
Nature Education, 1(1), 103.
• Kevin P Rice, Michael M Cox. (2001). Recombinational DNA Repair in Bacteria:
Postreplication . ENCYCLOPEDIA OF LIFE SCIENCES .
• Paweł Kowalczyk, Jolanta Krzyczkowska, Urszula Jankiewicz. (2013). MechanisMs of
the dna repair in bacterial and yeast cells. New Medicine, 1, 14-20.
• Sinha, R. P., & Häder, D. P. UV-induced DNA damage and repair: A review.
Photochemical and Photobiological Sciences 1, 225–236 (2002)
• Wiley-Liss. (2002). Mutation, Repair and Recombination. In B. TA, & 2nd (Ed.),
Genomes. Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK21114/
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 Thank you
Q&A
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