DNA REPAIR OVERVIEW

DNA Repair Overview

• DNA is a relatively stable molecule but can suffer damage from various sources.

Types of Damage to DNA

• Sources of Damage:

  • Thermal fluctuations (common)

  • Metabolic accidents (unintended oxidations)

  • Radiation (UV, X-ray)

  • Environmental toxins (mutagens, carcinogens)

• Note: These are different from replication errors.

DNA Repair Mechanisms

• Effectiveness: Approximately 99.9% of DNA damage is identified and repaired by cells.

• Function of Repair Proteins: Cells synthesize many repair proteins which often use a template for guidance, explaining the universality of double-stranded DNA as the hereditary material.

Common DNA Repair Mechanisms

• Base Excision Repair

• Nucleotide Excision Repair

• Double-Strand Break Repair

Base Excision Repair

• Process:

  • DNA glycosylases identify and separate damaged bases from DNA strands.

  • At least 6 different glycosylases exist, each recognizing specific altered bases.

  • When an altered base is detected, it leads to a conformational change and initiation of repair, where the base is removed via a hydrolytic reaction.

  • Other enzymes then remove the backbone of the strand, replacing the removed section with a new base.

• **Specific Enzymes: **

  • DNA Glycosylases: Remove damaged bases.

  • AP Endonuclease: Cuts one side of the sugar-phosphate bond.

  • Phosphodiesterase: Cuts the other side of the bond.

  • DNA Polymerase: Replaces the damaged base.

  • DNA Ligase: Seals the remaining bonds.

Base Chemistry Facilitating Repair

• Deamination: Refers to an altered base, involving a different glycosylase for each altered base.

• Note on Bases: Cytosine (C) can be deaminated to Uracil (U), resulting in DNA damage as U is typically not present in DNA.

Nucleotide Excision Repair (NER)

• Function: Repairs larger areas of damage, such as bulky lesions (e.g., covalent hydrocarbon attachments and dimerization).

• Mechanism:

  • A multi-enzyme complex binds to distorted regions on DNA.

  • Phosphodiester (PD) bonds around the lesion are cut allowing helicase to separate the damaged strand.

  • DNA polymerase and ligase then perform the repair.

Double-Strand Breaks (DSBs)

• Severity: DSBs are serious as both strands of the helix are damaged, complicating repair efforts.

• Repair Mechanism:

  • Non-Homologous End Joining (NHEJ): Simply rejoins broken ends, resulting in deletion mutations.

Homologous Recombination (HR)

• Characteristics:

  • Preserves the original DNA sequence, requiring a sister chromatid and occurs after replication (S and G2 phases).

  • Functional Mechanism: Involves single-stranded regions invading homologous double-stranded DNA.

  • Proteins involved: RecA (in E. coli) and RAD51 (in eukaryotes).

Recombination Processes

• Types:

  • Homologous recombination, transposition, and site-specific recombination involve DNA strand invasion.

  • Useful in repairing DSBs and allowing genetic exchange during meiosis (crossing over).

Consequences of Crossing Over

• Results: New combinations of alleles, gene conversion can occur leading to an unequal contribution of parental alleles.

Mobile Genetic Elements

• Move from one region of the genome to another, do not require homology between the sites, and can remain fixed in genomes (approx. 45% of human DNA).

Types of Transposable Elements

• Transposition: Involves both DNA-only and retroviral-like retrotransposons.

• Mechanism: DNA-only transposons utilize transposase; retrotransposons rely on reverse transcriptase for “copy and paste” movement between locations.

True Retroviruses

• Use a similar mechanism to retrotransposons but include proteins for moving between cells (e.g., viral coats).

Evolutionary Context

• All labeling of DNA repair, homologous recombination, and transpositional processes share similar biochemical mechanisms involving specific enzymes like endonucleases, exonucleases, and ligases.