DNA Damage and Repair
Introduction:
DNA repair ensures genetic integrity.
Failure in repair mechanisms can result in mutations, abnormal cell functions, cancers, and cell death.
Defective repair mechanisms are associated with genetic diseases.
DNA Damage:
DNA is susceptible to damage from external agents and replication errors.
If not repaired, damage leads to mutations.
Human cells experience 10,000 to 100,000 DNA modifications per cell per day.
Types of DNA Damage:
Depurination: Loss of purine bases, occurring about 10,000 times per day in a typical human cell.
Deamination: Converts cytosine to uracil, leading to a C/G to T/A transition.
Base Pair Transitions: Purine to purine or pyrimidine to pyrimidine replacement.
Base Pair Transversions: Purine to pyrimidine or vice versa.
Alkylation-Induced Mispairing: Addition of methyl or ethyl groups causing incorrect base pairing.
Intercalating Agents: Insertion between DNA bases leading to single nucleotide-pair insertions and deletions.
Photoproducts (Thymine Dimers): UV light induces covalent bonding between adjacent thymine bases.
Cellular Responses to DNA Damage:
Repair the DNA.
Arrest cell cycle if repair is not possible.
Induce apoptosis (cell death).
DNA Repair Mechanisms:
Proofreading by DNA Polymerases:
DNA Polymerase III checks and corrects errors during replication.
Features a 5→3 polymerase and 3→5 exonuclease activity.
Mismatch Repair (MMR):
Corrects replication errors missed by proofreading.
Involves scanning new DNA for mismatches and correcting them.
MMR defects are linked to hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch Syndrome.
Base Excision Repair:
Removes abnormal bases like uracil and repairs apurinic/apyrimidinic sites.
Involves glycosylases, AP-endonucleases, DNA polymerase, and ligase.
Nucleotide Excision Repair (NER):
Removes bulky DNA lesions caused by UV light, smoking, and chemicals.
Involves UvrABC exinuclease, which cuts out damaged segments and replaces them.
Double-Strand Break Repair:
Non-Homologous End-Joining (NHEJ): Directly ligates broken DNA ends but can be error-prone.
Homologous Recombination Repair: Uses a homologous DNA template for accurate repair, less error-prone.
Consequences of Faulty DNA Repair:
Mutations: Heritable changes in DNA causing various diseases.
Xeroderma Pigmentosum (XP):
Autosomal recessive disorder with extreme sensitivity to UV light.
Defects in NER lead to a high risk of skin cancers and other complications.
Symptoms include sun sensitivity, early onset freckling, neoplastic changes, and progressive neurological degeneration.
Summary of Repair Mechanisms:
Proofreading: Corrects replication errors.
Mismatch Repair: Fixes copying errors.
Base Excision Repair: Removes damaged bases and fills the gaps.
Nucleotide Excision Repair: Replaces damaged DNA segments.
Double-Strand Break Repair: Mends breaks in DNA using either NHEJ or homologous recombination.
Depurination
What is Depurination?
Depurination is a type of DNA damage where a purine base (adenine or guanine) is removed from the DNA molecule.
How Does it Happen?
The bond between the purine base and the sugar (deoxyribose) in the DNA backbone breaks. This bond is called a glycosidic bond.
What’s the Result?
The removal of the purine base leaves a gap or an empty spot in the DNA strand, known as an "abasic site" or "AP site" (apurinic site).
Why is it Important?
If not repaired, depurination can lead to mutations during DNA replication because the DNA polymerase might insert the wrong base opposite the empty spot.
Deamination
What is Deamination?
Deamination is a chemical change where an amino group (–NH2) is removed from a base in DNA.
How Does it Happen?
The removal of the amino group converts the base into a different base. For example:
Cytosine can be deaminated to become uracil.
Adenine can be deaminated to become hypoxanthine.
Guanine can be deaminated to become xanthine.
What’s the Result?
The altered bases can mispair during DNA replication, leading to mutations. For instance, uracil pairs with adenine instead of guanine.
Why is it Important?
If not corrected by repair mechanisms, deamination can cause permanent changes in the DNA sequence, leading to mutations which can contribute to diseases like cancer.
Summary
Depurination: Removal of a purine base (adenine or guanine) from DNA, leaving a gap that can cause mutations if not repaired.
Deamination: Removal of an amino group from a base in DNA, converting it into a different base that can mispair and cause mutations if not corrected.
What is Alkylation?
Alkylation is a process where an alkyl group (a group of carbon and hydrogen atoms) is added to a molecule. In the context of DNA, it means an alkyl group is added to one of the DNA bases.
How Does it Happen?
Chemicals called alkylating agents can attach alkyl groups to DNA bases. This can occur naturally or due to exposure to certain chemicals or drugs.
Which DNA Bases are Affected?
Alkylation can happen to any of the four DNA bases (adenine, thymine, cytosine, and guanine), but guanine is the most commonly affected.
What Happens to the DNA Bases?
When a base like guanine is alkylated, its structure changes. For example, guanine can be alkylated to form O^6-alkylguanine.
What’s the Result of This Change?
The altered base can mispair during DNA replication. Normally, guanine pairs with cytosine. However, alkylated guanine (O^6-alkylguanine) can pair incorrectly with thymine instead of cytosine.
Why is it Important?
This mispairing can lead to mutations when the DNA is replicated. If the mutation is not corrected by the DNA repair mechanisms, it can be passed on to the next generation of cells, potentially leading to various genetic diseases or cancer.
Summary
Alkylation: Addition of an alkyl group to DNA bases by alkylating agents.
Common Base Affected: Guanine, which can become O^6-alkylguanine.
Mispairing: Alkylated guanine can incorrectly pair with thymine instead of cytosine during DNA replication.
Consequence: This mispairing can cause mutations, which may lead to genetic diseases or cancer if not repaired.
What is Base Excision Repair (BER)?
BER is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is primarily responsible for fixing small, non-helix-distorting base lesions.
Why is it Needed?
DNA bases can get damaged by things like oxidative stress, alkylation, and deamination. These small damages can lead to mutations if not repaired.
How Does BER Work?
Step 1: Damage Recognition
A specialized enzyme called a DNA glycosylase scans the DNA and recognizes the damaged or incorrect base.
Step 2: Base Removal
The DNA glycosylase removes the damaged base, leaving an empty site called an "abasic site" or "AP site" (apurinic/apyrimidinic site).
Step 3: Cutting the DNA Backbone
An enzyme called AP endonuclease cuts the DNA backbone at the AP site to create a nick.
Step 4: Removing the Sugar
Another enzyme, such as a phosphodiesterase, removes the remaining sugar-phosphate backbone, leaving a clean gap.
Step 5: Filling the Gap
DNA polymerase adds the correct nucleotide to fill the gap.
Step 6: Sealing the DNA Strand
DNA ligase seals the nick in the DNA backbone, restoring the DNA to its correct form.
Why is BER Important?
BER helps maintain the integrity of the genetic information by correcting small, non-distorting damages to DNA. This prevents mutations and maintains cellular health.
Summary
Damage Recognition: DNA glycosylase finds and removes the damaged base.
Cutting the Backbone: AP endonuclease cuts the DNA at the empty site.
Removing the Sugar: The remaining sugar-phosphate backbone is removed.
Filling the Gap: DNA polymerase adds the correct base.
Sealing the DNA: DNA ligase seals the nick, completing the repair.