14.6 DNA Repair

DNA Mutations and Repair Mechanisms

DNA mutations are changes in genetic material that range from single nucleotide swaps to large-scale chromosomal rearrangements. These changes can alter protein function, disrupt gene expression, or sometimes have no effect at all. Understanding how mutations arise matters because they drive both genetic disorders and evolution.

Cells don't just accept this damage passively. They've evolved multiple repair mechanisms to maintain DNA integrity, including direct reversal, base excision repair, nucleotide excision repair, and mismatch repair. When these systems fail, the consequences can be severe, from cancer predisposition to degenerative diseases.

Types and Effects of DNA Mutations

Point mutations affect a single nucleotide position. There are three subtypes of substitution mutations, and they differ in how much damage they do:

• Silent mutation: The codon changes, but it still codes for the same amino acid. For example, GGG → GGA both code for glycine. The protein is unaffected because of redundancy in the genetic code.
• Missense mutation: The new codon specifies a different amino acid. GAG → GTG changes glutamic acid to valine. This is exactly what causes sickle cell anemia.
• Nonsense mutation: The new codon is a premature stop codon. CAG → TAG converts a glutamine codon into a stop signal, producing a truncated (and usually nonfunctional) protein.

Point mutations can also involve insertions (adding nucleotides) or deletions (removing nucleotides).

Frameshift mutations are the most disruptive type of point mutation. They occur when an insertion or deletion involves a number of nucleotides not divisible by three. Since the ribosome reads mRNA in triplets, adding or removing one or two nucleotides shifts the entire reading frame downstream. Every codon after the mutation is misread, usually producing a completely nonfunctional protein.

Chromosomal mutations are large-scale changes in chromosome structure or number:

• Deletions: Loss of a chromosome segment
• Duplications: Extra copies of a segment
• Inversions: A segment flips to reversed orientation
• Translocations: Segments exchange between non-homologous chromosomes

Potential effects of mutations vary widely:

• Altered protein structure or function (sickle cell anemia, where abnormal hemoglobin causes red blood cells to deform)
• Complete loss of protein function (cystic fibrosis, caused by a nonfunctional CFTR chloride channel)
• Gain of abnormal function (oncogenes that drive uncontrolled cell growth)
• Changed gene expression levels (thalassemia, where globin production is reduced)
• Progressive disease (Huntington's disease, caused by a trinucleotide repeat expansion)

Mechanisms of Cellular DNA Repair

Your cells face thousands of DNA lesions every day. Multiple repair pathways handle different types of damage.

Direct reversal fixes damage without removing any nucleotides:

• Photoreactivation: An enzyme called photolyase uses light energy to directly break apart UV-induced thymine dimers (pyrimidine dimers). This pathway exists in bacteria and many other organisms but is absent in placental mammals.
• Methyltransferases: These enzymes remove alkyl groups directly from damaged bases, such as $O^6$-methylguanine on guanine residues.

Base excision repair (BER) handles small, non-bulky lesions like oxidized or deaminated bases. The steps are:

1. A glycosylase recognizes and removes the damaged base (e.g., uracil or 8-oxoguanine), leaving an abasic site
2. AP endonuclease cleaves the DNA backbone at the abasic (apurinic/apyrimidinic) site
3. DNA polymerase fills in the gap with the correct nucleotide
4. DNA ligase seals the remaining nick in the backbone

Nucleotide excision repair (NER) handles bulky, helix-distorting lesions that BER can't fix, such as UV-induced cyclobutane pyrimidine dimers:

1. The distortion in the helix is recognized by repair proteins
2. An oligonucleotide segment containing the damage is excised (about 27–29 nucleotides in humans)
3. DNA polymerase fills the gap using the undamaged strand as a template
4. DNA ligase seals the nick

NER operates in two modes: transcription-coupled NER (prioritizes actively transcribed genes) and global genome NER (scans the entire genome).

Mismatch repair (MMR) catches errors that DNA polymerase's proofreading missed during replication:

1. Protein complexes (MutSα) recognize mismatched base pairs like G-T or A-C
2. The system identifies which strand is the newly synthesized one (using nicks as strand-discrimination signals)
3. The section of the new strand containing the mismatch is excised
4. DNA polymerase resynthesizes the excised region, and ligase seals the nick

Double-strand break repair addresses the most dangerous type of DNA damage, where both strands are severed:

1. Homologous recombination (HR): Uses the sister chromatid as a template to accurately rebuild the broken region. This is error-free but requires a sister chromatid, so it mainly operates during S and G2 phases of the cell cycle.
2. Non-homologous end joining (NHEJ): Directly ligates the broken ends back together without a template. This is faster but error-prone because nucleotides can be lost or added at the junction.

Key Enzymes in DNA Repair

• DNA polymerases: Synthesize new DNA to replace damaged or excised segments. Some also have proofreading ability (3' → 5' exonuclease activity) that catches replication errors before they become permanent.
• DNA ligases: Seal nicks in the sugar-phosphate backbone after repair synthesis is complete.
• Helicases: Unwind the double helix so repair enzymes can access the damaged region.
• Topoisomerases: Relieve torsional stress that builds up when DNA is unwound during repair.

DNA Repair Defects and Disease

When repair pathways are compromised by inherited mutations, the results can be devastating. Each disease below maps to a specific repair pathway failure.

Xeroderma pigmentosum (XP) results from defects in nucleotide excision repair genes (XPA through XPG). Affected individuals are extremely sensitive to UV light and face roughly a 1,000-fold higher risk of skin cancers, including basal cell carcinoma, squamous cell carcinoma, and melanoma. This disease is a direct illustration of why NER matters.

Hereditary nonpolyposis colorectal cancer (HNPCC/Lynch syndrome) is caused by defects in mismatch repair genes, most commonly MSH2 and MLH1. It follows an autosomal dominant inheritance pattern. Lifetime risk of colorectal cancer can reach up to 80%, with elevated risk of endometrial and other cancers as well.

Ataxia telangiectasia (AT) stems from mutations in the ATM gene, which encodes a kinase critical for the double-strand break response and cell cycle checkpoints. Symptoms include progressive neurodegeneration, immunodeficiency, and predisposition to leukemia and lymphoma.

Fanconi anemia (FA) involves defects in genes responsible for repairing DNA interstrand crosslinks (FANCA, FANCB, FANCC, and others). It leads to bone marrow failure, congenital abnormalities, and increased risk of acute myeloid leukemia.

Bloom syndrome (BS) is caused by mutations in the BLM gene, which encodes a RecQ helicase involved in homologous recombination. It results in growth retardation, immunodeficiency, and broad cancer predisposition spanning leukemia, lymphoma, and solid tumors.