DNA DAMAGE AND
REPAIR
Molecular cell biology
Hifsa zia
MPhil Microbiology
Definition
• DNA damage refers to any structural alteration or modification in the
DNA molecule (chemical structure) that affects its integrity, stability,
or function. These changes can interfere with replication and
transcription, potentially leading to mutations, genomic instability, or
cell death. If left unrepaired, DNA damage can contribute to diseases
like cancer and neurodegeneration.
Causes of DNA damage
• Endogenous (Internal) Sources
• Reactive Oxygen Species (ROS): Byproducts of cellular metabolism
that attack DNA.
• Replication Errors: Mistakes made during DNA synthesis.
• Spontaneous Hydrolysis: Leads to base loss (depurination) or
incorrect base conversion (deamination).
Exogenous (External) Sources
• Ultraviolet (UV) Radiation: Causes pyrimidine dimers.
• Ionizing Radiation (X-rays, Gamma rays): Induces strand breaks.
• Chemical Mutagens: Alkylating agents, benzopyrene, aflatoxins, etc.
• Chemotherapy & Radiotherapy: Induce DNA damage in cancer cells.
Types of DNA Damage
1-Single-Strand Breaks (SSBs)
• Occur when only one strand of the
DNA double helix is broken.
• Caused by oxidative stress, ionizing
radiation, or certain chemicals.
• Most common type of DNA damage
2-Double-Strand Breaks (DSBs)
• Both strands of the DNA helix are broken.
• Highly dangerous, as they can lead to
chromosomal rearrangements and
mutations.
• Caused by ionizing radiation, replication
stress, and reactive oxygen species.
3-Base Modifications &
Oxidative Damage
• Chemical alterations to individual DNA bases.
• Example: 8-oxo-guanine, caused by oxidative stress, can lead to
incorrect base pairing during replication.
4-Pyrimidine Dimers (UV
Damage)
• Caused by ultraviolet (UV) radiation.
• Covalent bonds form between adjacent
pyrimidine bases (thymine or cytosine),
distorting the DNA structure and
blocking replication/transcription.
5-Interstrand Crosslinks (ICLs)
• Covalent links form between
complementary DNA strands.
• Prevent strand separation, interfering
with replication and transcription.
• Caused by chemotherapy drugs (e.g.,
cisplatin) and environmental toxins.
6-Mismatched Bases &
Replication Errors
• A base-pairing error in DNA that occurs when a base
pairs incorrectly with another base, Such as pairing A with
C or G with T instead of A-T and G-C.
• Occur due to mistakes made by DNA polymerase during replication.
• If not corrected by mismatch repair (MMR), they can lead to
permanent mutations.
DNA REPAIR
1-Nucleotide excision repair (NER)
• Nucleotide excision repair (NER) operates by a cut-and patch
mechanism that removes a variety of bulky lesions, including
pyrimidine dimers and nucleotides to which various chemical groups
have become attached.
• Two distinct NER pathways can be distinguished
I. Transcription-coupled pathway
• A transcription-coupled pathway in which the template strands of
genes that are being actively transcribed are preferentially repaired.
• It specifically repairs DNA damage in actively transcribed genes,
ensuring that essential genes are quickly restored to prevent
transcriptional blockage.
II.Global Genomic NER (GG-NER)
• Global Genomic NER (GG-NER) is a sub-pathway of Nucleotide
Excision Repair (NER) that removes bulky, helix-distorting lesions
(such as UV-induced pyrimidine dimers or chemical adducts) from the
entire genome, including both transcribed and non-transcribed
regions.
• It is a slower, less efficient process
2-Base excision repair (BER)
• Base excision repair (BER) is a cellular mechanism that primarily repairs small, non-helix-
distorting DNA base lesions caused by oxidation, alkylation, or deamination, by removing
the damaged base and replacing it with a new one, thus maintaining genome integrity
• BER is initiated by a DNA glycosylase that recognizes the alteration
• A number of different DNA glycosylases have been identified, specific for a particular type
of altered base.
• Examples uracil (formed by the hydrolytic removal of the amino group of cytosine) and 8-
oxoguanine (caused by damage from oxygen free radicals).
Mechanism
1. Damage Recognition: DNA Glycosylase recognizes the damaged base
2. AP Site Processing: AP Endonuclease 1 (APE1) cuts the DNA backbone
at the abasic site, creating a single-strand break.
3. DNA Synthesis and Repair: Two BER Sub-pathways Exist
I. Short Patch BER (1 nucleotide replacement): DNA Polymerase β
inserts a single correct nucleotide.
II. Long Patch BER (2-10 nucleotide replacement): DNA Polymerase δ/ε
synthesizes a longer DNA strand, displacing the damaged fragment.
4. DNA Ligase III (Short Patch) or DNA Ligase I (Long Patch) seals the
repaired DNA strand.
3-Mismatch Repair (MMR)
• Mismatch Recognition: there are some enzymes which scan the newly
synthesized DNA strand for mismatches
• Identification of the Newly Synthesized Strand: In bacteria, hemimethylated
DNA and in eukaryotes, the strand is identified by nicks (gaps) left by lagging
strand synthesis.
• Exonuclease 1 (EXO1) removes a section of the newly synthesized strand
containing the mismatch.
• DNA Synthesis and Ligation:
• DNA Polymerase fills in the missing nucleotides using the parental strand as
a template.
• DNA Ligase I seals the final gap to complete the repair.
4-Double-strand breakage repair
• Double-strand breaks (DSBs) are the most severe form of DNA
damage and can lead to genomic instability, mutations, and cell death
if not repaired properly
• There are two pathway for double strand breakage repair
I- Non- homologous end joining
• The lesion is detected by a heterodimeric, ring-shaped
• protein called Ku, that binds to the broken ends of the DNA
• The DNA-bound Ku recruits another protein, called DNA-PKcs, which
is the catalytic subunit of a DNA-dependent protein kinase
• These proteins bring the ends of the broken DNA together in such a
way that they can be joined by DNA ligase IV to regenerate an intact
DNA duplex
II-
