Major Types of Genetic Material Damage
Every day, the genomic structure is subjected to attacks by external and internal factors, including radiation, chemical agents, and ultraviolet (UV) radiation. This leads to various defects that are normally repaired by specific enzymes.
The following types of DNA damage are recognized:
- Base deamination: Spontaneous loss of an amino group. Most commonly, cytosine is converted to uracil. Adenine can convert to hypoxanthine, and guanine to xanthine.
- Loss of nitrogenous bases: A hydrolytic process of depurination or depyrimidination where the base is cleaved off, leaving an empty deoxyribose residue.
- Pyrimidine dimers: Covalent cross-linking of adjacent bases on the same strand induced by UV radiation.
- Nucleotide strand breaks and replication errors.
- Covalent cross-links: Between two complementary DNA strands or between DNA and histone proteins.
- DNA alkylation: Attachment of alkyl groups due to chemical exposure (e.g., formation of 3-methyladenine, 6-methylguanine, or 7-methylguanine).
Restoring a Strand Following Base Loss
If hydrolytic cleavage of a purine or pyrimidine base occurs, a specific defect forms in the strand. The cell can use two main pathways to resolve this.
- The first pathway is the direct action of DNA insertase. This enzyme can independently attach the missing nitrogenous base to the empty deoxyribose, strictly following the rule of complementarity.
- The second, more complex pathway is excision repair. In this case, the enzyme AP endonuclease (apurinic/apyrimidinic) acts by detecting the base-free deoxyribose site and hydrolyzing the 3',5'-phosphodiester bond, creating a nick in the sugar-phosphate backbone for subsequent processing by the entire repair complex.
Steps of DNA Excision Repair
The elimination of damaged regions (excision) in eukaryotes requires a coordinated and strict sequence of enzymatic actions.
Sometimes the initial step involves DNA N-glycosylase, which recognizes the chemically modified base and hydrolyzes the N-glycosidic bond, leaving an apurinic/apyrimidinic (AP) site. The subsequent process of filling the gap follows a clear sequence:
- Damage site recognition: An endonuclease finds the defect and hydrolyzes the phosphodiester bond, nicking the damaged strand.
- Excision (removal): An exonuclease locates the break and neatly cuts out the defective nucleotides from the strand.
- Synthesis (filling): DNA polymerase $\beta$ binds to the 3'-end of the resulting gap. Using deoxynucleoside triphosphates (dNTPs) and strictly guided by the undamaged complementary template strand, it synthesizes the missing fragment. This reaction releases inorganic pyrophosphate ($PP_i$).
- Ligation: The enzyme DNA ligase permanently seals the newly synthesized fragment with the main undamaged section. This process requires energy, so an ATP molecule is cleaved to AMP and $PP_i$.
Biological Basis of Reliability
The primary principle ensuring the possibility of error correction is the presence of two strands in the DNA molecule, representing two copies of genetic information. The second strand always serves as a reliable template for repairing the defect.
However, critical situations occur when both nucleotides in a complementary pair are damaged simultaneously. In this case, the outcome depends on the cell type:
- In haploid cells, repair of such damage becomes impossible due to the lack of a backup copy of information for accurate synthesis.
- In diploid cells, the repair system can restore the structure using the identical undamaged gene located on the homologous chromosome.