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Figure 4.11 Consequences of deamination, depurination, and oxidation. Cytidine is deaminated, resulting in uracil that then pairs with adenine during replication. If a depurinated nucleotide is not repaired, DNA polymerase passes over the depurinated position during replication. A point deletion that can lead to frameshift mutations results.
In rare cases, the bases can be present in a tautomeric form (Figure 4.12). If they are selected during replication, they can lead to point mutations. G and T are normally present in the keto form and very rarely take the enol form. The amino group of A and C can in rare cases convert into an imino function. Tautomeric adenine pairs with cytosine instead of with thymine; tautomeric thymine pairs with guanine instead of with adenine and vice versa. The resulting nucleotide substitutions fall into the class of the transitions. This includes substitutions of pyrimidine bases with another pyrimidine (T to C or vice versa) and the substitution of a purine base by another (A → G or vice versa). Transversions include the exchange of a purine base with a pyrimidine (A → C or T/G → C or T and vice versa).
Figure 4.12 Base pairing of tautomeric DNA bases. The correct base pairings for A–T and G–C pairs are illustrated in (a). Base pairs between tautomers A, G, C, and T are shown in (b) and (c).
Most of the primary gene changes (deamination, depurination, dimerization, and oxidation) are recognized by repair enzymes (such as AP endonuclease and DNA glycosylases), cut out (as long as the second DNA strand is not also damaged), and repaired by DNA polymerase (especially translesion polymerases) and DNA ligase. In addition, alkyltransferases, photolyases, and incorrect pairing repair and recombination repair systems (see homologous recombination) are also available, which are active after replication. The double helix is also advantageous for any repair process, as genetic information is complementarily saved. Even if the information on one strand is lost, the complementary strand is still available and can be used as a template for the needed correction. In gametes, such as those of humans, thanks to the effectiveness of the repair systems, there are only 10–20 nucleotide substitutions per year in relation to the available 3.2 × 109 bases. The significance of the repair system is easily recognized in humans who are affected by xeroderma pigmentosum, a rare autosomal recessive neurocutaneous disease, in which certain elements of the repair system that are required to repair DNA damage caused by UV radiation do not function. As a result of mutagenic UV radiation from sunlight, aside from numerous neurological and psychiatric symptoms, skin discoloration and skin cancer can occur. This can only be prevented by complete avoidance of sunlight. Table 4.5 lists further diseases caused by defective repair enzymes.
Table 4.5 Genetic diseases, which are associated with defective DNA repair systems.
| Syndrome | Phenotype | Damaged proteins |
|---|---|---|
| MH2,3,6; MLH1; PMS2 | Colon cancer | Mismatch repair |
| Xeroderma pigmentosum (XP) | Skin cancer, neurological disorders | Excision repair |
| Cockayne syndrome | UV sensitivity, developmental abnormalities | Coupling of nucleotide excision repair to transcription |
| XP variant | UV sensitivity, skin cancer | Translesion synthesis by DNA polymerase |
| BRCA1 | Breast and ovarian cancer | Repair through homologous recombination |
| BRCA2 | Breast, ovarian, and prostate cancer | Repair through homologous recombination |
| Werner syndrome | Premature aging, many tumors | 3‐Exonuclease, DNA helicase for DNA repair |
| Bloom syndrome | Many tumors, stunted growth, genome instability | DNA helicase for DNA repair |
| Fanconi anemia groups A–G | Malformations, leukemia, genome instability | DNA interstrand cross‐link repair |
| 46 BR‐patient | Hypersensitivity for mutagenic substances, genome instability | DNA ligase I |
Source: Alberts et al. (2015). Reproduced with permission of Garland Science.
Owing to the redundant genetic code, not every point mutation in a gene leads to a change in the amino acid sequence. Twenty‐five percent of all theoretically possible substitutions are synonymous, 4% lead to stop codons, and 71% to amino acid exchange. Nucleotide substitutions in the third codon position do not lead to a change in the amino acid in about 69% of cases (referred to as a silent mutation). Should deletions or insertions occur within a coded sequence, a frameshift mutation results, which almost always leads to severe damage of the corresponding proteins (Figure 4.13).
Figure 4.13 Consequences of gene mutations.
Point mutations that cause amino acid exchange (nonsynonymous substitution) often have a negative effect on the corresponding proteins. If the mutation is in the active site or in a binding site, a total loss of function can result. As diploid organisms have at least two copies of every gene, positioned on autologous chromosomes, such a point mutation usually does not lead to physical damage if the other copy of the gene is still intact. Only after both copies have been damaged is there a loss of the corresponding protein function (Figure 4.14). Such disruption is often the basis for disease. This is especially true when the mutation arises in gametes and is then inherited. If the disorder is only in one allele, then it is referred to as a heterozygote character. If both alleles are identical, this is known as a homozygote character (Figure 4.14). In certain genes, such point mutations and the consequences on the health of the individual are widely known. They are referred to as SNPs (single nucleotide polymorphisms), if they occur in several individuals of a population. One of the most important tasks for molecular biotechnologists is the development of diagnostic systems to quickly and reproducibly detect such SNPs. For this purpose mass spectrometry, DNA sequencing, NGS, PCR methods,