## Endogenous causes of DNA damage

Among the changes that occur spontaneously due to the chemical properties of DNA are tautomeric rearrangements and errors in DNA replication. Tautomeric shifts are spontaneous rearrangements that involve the transfer of hydrogen atoms within a base, resulting in a non-standard base that will have altered pairing. For example, it is usual for cytosine (an amino) to pair with guanine (a keto), but when a tautomeric rearrangement occurs within the cytosine molecule this results in the formation of the less abundant imino form of cytosine, which means it can pair with adenine (Figure 5.3). Such a change in the base pairing cannot be considered a mutation because the cell can repair it, but such pairing presents a problem that must be resolved before the next replication. If the alternate form of the base cannot be solved, a mutation already occurs after replication, where the original C-G pair is replaced by a T-A pair (termed a transition mutation).

Similarly, a mutation can also occur during DNA replication when the enzyme DNA polymerase inserts an incorrect nucleotide, adds an extra nucleotide or even omits one. In all of these cases, a mismatched base pair is created, which the cell can still repair – but only if the mismatch is recognised quickly. Since DNA damage is a very serious change, the enzyme DNA polymerase itself is able to recognize and repair mismatched/damaged bases. However, if the cell fails to recognize a mismatch base pair, a mutation called a base substitution will result after the next round of replication (Figure 5.4). A base substitution can have different effects on the cell depending on which substitution has occurred. As mentioned in Chapter 3 – Get to know DNA as the carrier of genetic information, DNA is transcribed into an mRNA sequence during transcription, which is subsequently translated into the amino acid sequence for the protein during translation. Each nucleotide triplet in the mRNA, called a codon, defines one of the 20 standard amino acids that can be part of a protein chain. However, an amino acid can be encoded by more than one codon, so for example serine can be coded by the codon AGU and AGC. In our example (Figure 5.4), phenylalanine is coded by UUU, but a single base swap mutation that turns the codon to UUC has no obvious effect, as both codons result in phenylalanine being added to the sequence. We refer to such a mutation as a silent, or synonymous, mutation. In the case of a non-synonymous mutation, the original amino acid is replaced by another. If this is an amino acid with similar properties to the original one, the resulting effect may not have serious consequences - then it is a neutral mutation. However, if an amino acid with different properties is incorporated, such as a mutation from UUU to UUA resulting in leucine in place of phenylalanine, the resulting protein may not function properly, which is called a missense mutation. A substitution, or base insertion, that results in the formation of a premature STOP codon (a so-called nonsense mutation) causes premature termination of translation and the formation of a truncated protein. Another error that can occur during DNA replication is the insertion or deletion of one or more nucleotides. In this case, it is the so-called shift mutation because it shifts the reading of the genetic code (Figure 5.4). Such a change has more severe effects on the cell because the shift in the reading of the genetic code at the site where the nucleotide was inserted results in a completely different protein.