DNA REPAIR

It can be defined as “any one of the cellular process that attempts to correct errors in cellular DNA which occurred during cell division or by external environment”. There are many cellular proteins and enzymes which help in repairing most of the errors by means of different mechanisms.

Photoreactivation

• Catalyzed by DNA-Photolyase (DPL)
• Reverses cyclobutyl pyrimidine dimers resulting from UV irradiation.
• It has low abundance (10 to 20 molecules per cell) in E. coli.
• DPL binds irradiated DNA 100x better than non-irradiated DNA.
• DPL contains a non-covalently associated chromophore (FADH or FADH2).
• The photochemical mechanism of photorepair has been proposed to be light-dependent redox reaction between the singlet excited state of FADH2 and the pyrimidine dimer.
• Photolyase has not yet been identified in placental mammals.

Trp Operon:

Fig. 28. Photoreactivation

Aberrant Methylation

• Catalyzed by 6-O-methylguanine methyltransferase (6-O-MGM)
• 6-O-MGM recognizes 6-O-methylguanine in DNA and removes the methyl group, transferring the group to an amino acid on itself in a "suicide" mechanism.
• 6-O-MGM is encoded by the ada gene in E. coli and the MGMT gene in eukaryotes.
• Mice knocked out for MGMT are cancer-prone and sensitive to methylation agents

Common Features of Excision-Type Repair Pathways

• Recognition: Altered DNA is recognized and bound by a specific damage-recognition protein. This first step recruits other components required for the repair reaction.
• Excision: Damaged base(s), and in some cases adjacent nucleotides, are excised from the strand by exonucleases, resulting in a gapped DNA.
• Resynthesis: The gap is refilled by a DNA polymerase using the complementary strand as a template.

Base-Excision Repair (BER)

• Damaged bases are removed as free bases.
• BER primarily handles oxidative and alkylative damage.
• BER is thought to have an important role in aging.
• BER recognizes base deamination, oxidative damage, and other minor base modifications.
• Five gene products are required for BER: glycosylase, AP endonuclease, phosphodiesterase, DNA polymerase, and DNA ligase.
• DNA glycosylase recognizes the damaged base and removes it, generating an AP (apurinic, apyramidinic) site.
• AP endonuclease cleaves the phosphodiester bond, generating a single-strand break with a 5'-terminal deoxyribophosphate moiety.
• The 5'-deoxyribophosphate is excised by action of a DNA phosphodiesterase.
• The resulting single-nucleotide gap is repaired by DNA polymerase β (beta).
• The resulting nick is sealed by DNA ligase.
• BER is relatively inefficient, due to the large number of peptides needed to recognize each damage type.