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Mutations do not occur randomly in the sense of “completely without cause”; they usually arise from identifiable physical, chemical, or biological influences, or from errors in normal cell processes. In this chapter, the focus is on why DNA changes arise, not on how they are inherited or what forms they take (which belong to other sections).
We distinguish broadly between:
- Spontaneous mutations – arise without an obvious external trigger, from “natural” processes in the cell.
- Induced mutations – arise because of external mutagens such as radiation or chemicals.
Both ultimately act by changing the DNA sequence or structure.
Spontaneous Causes of Mutations
Spontaneous mutations occur during normal life processes, even in a stable environment. They are unavoidable “background noise” of DNA chemistry and cell function.
1. Errors During DNA Replication
During DNA replication, DNA polymerases copy billions of bases with very high, but not perfect, accuracy.
- Mismatched base incorporation
A wrong nucleotide can be added (e.g. inserting G instead of A). Proofreading and DNA repair correct most of these errors, but some escape and become permanent mutations after the next round of replication. - Replication slippage (especially in repetitive sequences)
In regions with repeated short sequences (e.g.CACACACAorCAGCAGCAG), the polymerase can “slip”: - A loop on the new strand can lead to an insertion (extra repeat).
- A loop on the template strand can lead to a deletion (missing repeat).
This is common in “microsatellites” and can produce rapid length changes in these regions.
2. Spontaneous Chemical Changes of Bases
Even without external mutagens, bases in DNA are chemically unstable and undergo rare spontaneous reactions.
a) Depurination and Depyrimidination (Loss of Bases)
- Depurination: loss of a purine base (A or G) from the sugar-phosphate backbone.
- Depyrimidination: analogous loss of a pyrimidine base (C or T), less frequent than depurination.
This leaves an abasic site (no base). During replication, DNA polymerase must “guess” which base to insert opposite the empty site, often resulting in a base substitution.
b) Deamination (Loss of Amino Groups)
Deamination converts one base into another:
- Cytosine → uracil (U)
Uracil is not normally present in DNA. If not repaired, replication can pair U with A, converting an original C–G pair into a T–A pair in descendants. - 5-methylcytosine → thymine
This is particularly important because: - 5-methylcytosine occurs in many genomes as part of epigenetic regulation.
- Deamination produces thymine, which is a normal DNA base and more difficult to recognize as “wrong.”
- This mechanism explains why certain DNA sequences (e.g. CpG sites) are “mutation hot spots.”
Other deaminations (A → hypoxanthine, G → xanthine) also disturb pairing but are often repaired.
3. Tautomeric Shifts and Base Mispairing
DNA bases can rarely and briefly adopt alternative tautomeric forms (slightly different positions of hydrogen atoms). In such forms, a base can pair abnormally:
- A (rare tautomer) may pair with C instead of T.
- C (rare tautomer) may pair with A instead of G.
Normally, these rare forms revert quickly, but if a replication fork passes while a base is in its rare tautomeric state, a transient mispairing can become a permanent point mutation in the next generation of DNA.
4. Errors in DNA Repair and Recombination
Cells continually repair DNA damage. Sometimes the repair itself introduces mutations:
- Error-prone repair polymerases: when DNA is heavily damaged, some organisms use special polymerases that can bypass lesions but are inaccurate, leading to a high mutation rate.
- Misrepair of double-strand breaks:
- Joining the wrong ends can lead to deletions, insertions, inversions, or translocations of chromosomal segments.
- Imprecise recombination:
- During crossing-over in meiosis, misalignment of similar but non-identical sequences can cause unequal exchange, leading to duplications in one chromosome and deletions in the other.
Thus, processes intended to maintain genome integrity can sometimes be sources of mutation.
Induced Causes of Mutations
Induced mutations result from exposure to mutagens – physical or chemical agents that increase the frequency of DNA damage or replication errors. Some mutagens are also carcinogens (cancer-causing).
1. Physical Mutagens: Radiation
a) Ionizing Radiation
Ionizing radiation has enough energy to remove electrons from atoms and molecules:
- Examples: X-rays, gamma rays, high-energy particles (alpha, beta, cosmic rays).
- Primary effects:
- Single-strand breaks and double-strand breaks in DNA.
- Base damage and sugar-phosphate backbone damage through formation of reactive radicals, especially from water (e.g. hydroxyl radicals).
Consequences:
- Incorrect repair of breaks can cause deletions, inversions, translocations, and sometimes chromosome fragmentation.
- Base damage and misrepair can also cause point mutations.
Because double-strand breaks are dangerous, cells expose to high doses of ionizing radiation often undergo cell death; survivors may carry complex mutations.
b) Non-ionizing Radiation: Ultraviolet (UV) Light
UV radiation, especially UV-B and UV-C, is strongly absorbed by DNA bases:
- Major lesion: pyrimidine dimers, especially thymine dimers
Adjacent thymine (or cytosine) bases on the same strand can covalently link, forming a dimer that distorts the DNA helix.
If not correctly removed and replaced:
- DNA polymerase can stall or misread the dimer.
- Mutagenic “bypass” synthesis may insert incorrect bases, leading to base substitutions or small insertions/deletions.
Organisms have specific repair systems for UV damage; failure of these systems leads to extreme UV sensitivity and high mutation rates in exposed tissues.
2. Chemical Mutagens
Chemical mutagens interact with DNA or its precursors to change base pairing or the structure of the DNA molecule.
a) Base Analogs
Base analogs are molecules similar to normal bases that can be incorporated into DNA in their place but have unusual pairing properties.
- Example: 5-bromouracil (5-BU), an analog of thymine:
- Can pair with A in one tautomeric form.
- Can mispair with G in another form.
- Result: increased frequency of transition mutations (purine ↔ purine, pyrimidine ↔ pyrimidine).
Base analogs often act during DNA replication and are especially mutagenic in rapidly dividing cells.
b) Base-Modifying Agents
These chemicals react with existing bases and alter their chemical structure, changing their pairing behavior.
- Deaminating agents
- Example: nitrous acid (HNO₂)
- Converts cytosine to uracil, adenine to hypoxanthine.
- These modified bases pair incorrectly during replication, causing point mutations.
- Alkylating agents
- Transfer alkyl groups (e.g. methyl, ethyl) to bases or the DNA backbone.
- Examples: ethyl methanesulfonate (EMS), methyl methanesulfonate (MMS), certain chemotherapy drugs.
- Effects:
- Alkylated guanine (e.g. O⁶-ethylguanine) may pair with T instead of C → G·C → A·T transitions.
- Heavier alkylation can lead to strand breaks and larger chromosomal changes.
c) Intercalating Agents
Intercalating agents are flat, ring-shaped molecules that insert themselves between stacked base pairs in the DNA double helix.
- Examples: ethidium bromide, acridine dyes, proflavine.
- Insertion distorts the DNA helix and affects replication:
- DNA polymerase may add or skip a base opposite the intercalated molecule.
- Result: single-base insertions or deletions (indels), especially in single-base-repeat or short-repeat regions.
Indels in coding sequences can cause frameshift mutations, drastically altering the resulting protein.
d) Crosslinking Agents and DNA-Binding Chemicals
Some chemicals form covalent crosslinks:
- Between two bases on the same strand or on opposite strands.
- Between DNA and proteins.
Examples:
- Psoralens (activated by UV), used experimentally.
- Several chemotherapeutic drugs (e.g. cisplatin) for cancer treatment.
Consequences:
- Replication forks stall at crosslinked regions.
- Error-prone repair or misrepair can yield deletions, rearrangements, or multiple nearby base changes.
3. Biological Agents as Mutagens
Living organisms or their components can also promote mutations.
a) Transposable Elements (“Jumping Genes”)
Transposable elements are DNA sequences that can move within the genome:
- They may encode enzymes (transposases, integrases) that cut and reinsert their DNA.
- Movement can:
- Insert the element into a gene or regulatory region (often inactivating or altering it).
- Create breaks and recombination hotspots.
- Lead to duplications, deletions, or inversions of adjacent sequences.
In many organisms, transposable elements are a major source of spontaneous genetic variation.
b) Viruses and Viral Integration
Some viruses, particularly retroviruses and certain DNA viruses, integrate their genome into host DNA:
- The viral insertion can:
- Disrupt host genes or regulatory regions.
- Activate or inactivate nearby genes (e.g. by viral promoters or enhancers).
- Introduce new sequences that promote recombination or chromosomal instability.
This can lead to insertional mutagenesis and sometimes to cancer if key regulatory genes are affected.
c) Reactive Oxygen Species (ROS) from Metabolism
Cells continuously generate reactive oxygen species during normal respiration and other metabolic reactions:
- Examples: superoxide anion, hydrogen peroxide, hydroxyl radicals.
- ROS attack DNA bases and the sugar-phosphate backbone.
Common lesion:
- 8-oxoguanine (8-oxoG) from oxidation of guanine:
- 8-oxoG can pair with A instead of C, leading to G·C → T·A transversions when replicated.
Although cells have antioxidant systems and repair enzymes to counter ROS, some oxidative damage escapes repair and causes mutations.
Factors Influencing Mutation Rates
While the basic mechanisms above are universal, the actual mutation rate depends on several factors:
- DNA repair efficiency
Organisms with highly efficient and accurate repair systems show lower mutation rates; defects in repair genes often greatly increase mutation frequency. - Replication rate and number of cell divisions
More DNA replication events → more opportunities for replication errors and for lesions to be miscopied. - Genome composition and structure
- Regions rich in certain sequences (e.g. methylated CpG, repeats) are particularly prone to specific mutations.
- Compact vs. open chromatin can modulate exposure to damage and repair access.
- Environmental exposure
- Level and duration of exposure to UV, ionizing radiation, mutagenic chemicals, and certain biological agents.
- Lifestyle factors (e.g. smoking, diet) in humans affect exposure to mutagens.
Summary: From Cause to Mutation
Mutations arise because DNA is both:
- Chemically reactive in normal conditions (leading to spontaneous lesions and mispairing), and
- Physically and chemically vulnerable to environmental agents (mutagens).
The main categories of causes are:
- Spontaneous:
- Replication errors and slippage.
- Spontaneous base loss (depurination, depyrimidination).
- Deamination and other base modifications.
- Tautomeric shifts and mispairing.
- Errors in repair and recombination.
- Induced:
- Physical mutagens: ionizing radiation, UV radiation.
- Chemical mutagens: base analogs, base-modifying agents, intercalating agents, crosslinkers.
- Biological mutagens: transposable elements, integrating viruses, ROS from metabolism.
The type of change in the DNA sequence or in chromosome structure produced by these causes is treated in detail in the chapter on Types of Mutations.