DNA is a relatively stable molecule but can suffer damage from various sources.
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.
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.
Base Excision Repair
Nucleotide Excision Repair
Double-Strand Break 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.
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.
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.
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.
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).
Types:
Homologous recombination, transposition, and site-specific recombination involve DNA strand invasion.
Useful in repairing DSBs and allowing genetic exchange during meiosis (crossing over).
Results: New combinations of alleles, gene conversion can occur leading to an unequal contribution of parental alleles.
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).
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.
Use a similar mechanism to retrotransposons but include proteins for moving between cells (e.g., viral coats).
All labeling of DNA repair, homologous recombination, and transpositional processes share similar biochemical mechanisms involving specific enzymes like endonucleases, exonucleases, and ligases.