Mutations can result from chemical or physical events that lead to base modification. When they affect the base-pairing pattern, they interfere with replication or transcription. Chemical
substancees able to induce such changes are called mutagens. Mutagens cause mutations in different ways. Spontaneous oxidation, hydrolysis, uncontrolled methylation, alkylation, and ultraviolet irradiation result in alterations that modify nucleotide bases. DNA-reactive chemicals change nucleotide bases into different chemical structures or remove a base.
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A. Deamination and methylation
Cytosine, adenine, and guanine contain an amino group. When this is removed (deamination), a modified base with a different basepairing pattern results. Nitrous acid typically removes the amino group. This also occurs spontaneously at a rate of 100 bases per genome per day (Alberts et al., 1994, p. 245). Deamination of cytosine removes the amino group in position 4 (1). The resulting molecule is uracil (2). This pairs with adenine rather than guanine. Normally this change is efficiently repaired by uracil-DNA glycosylase. Deamination at the RNA level occurs in RNA editing (see Expression of genes). Methylation of the carbon atom in position 5 of cytosine results in 5 methylcytosine, containing a methyl group in position 5 (3). Deamination of 5-methylcytosine will result in a change to thymine, containing an oxygen in position 4 instead of an amino group (4). This mutation will not be corrected because thymine is a natural base. Adenine (5) can be deaminated in position 6 to form hypoxanthine, which contains an oxygen in this position instead of an amino group (6), and which pairs with cytosine instead of thymine. The resulting change after DNA replication is a cytosine instead of a thymine in the mutant strand.
About 5000 purine bases (adenine and guanine) are lost per day from DNA in each cell (depurination) owing to thermal fluctuations. Depurination of DNA involves hydrolytic cleavage of the N-glycosyl linkage of deoxyribose to the guanine nitrogen in position 9.This leaves a depurinated sugar. The loss of a base pair will lead to a deletion after the next replication if not repaired in time (see DNA repair).
Alkylation is the introduction of a methyl or an ethyl group into a molecule. The alkylation of guanine involves the replacement of the hydrogen bond to the oxygen atom in position 6 by a methyl group, to form 6-methylguanine. This can no longer pair with cytosine. Instead, it will pair with thymine. Thus, after the next replication the opposite cytosine (C) is replaced by a thymine (T) in the mutant daughter molecule. Important alkylating agents are ethylnitroso urea (ENU), ethylmethane sulfonate (EMS), dimethylnitrosamine, and N-methyl-N-nitroN-nitrosoguanidine.
D. Nucleotide base analogue
Base analogs are purines or pyrimidines that are similar enough to the regular nucleotide DNA bases to be incorporated into the new strand during replication. 5-Bromodeoxyuridine (5BrdU) is an analog of thymine. It contains a bromine atom instead of the methyl group in position 5.Thus, it can be incorporated into the new DNA strand during replication. However, the presence of the bromine atom causes ambiguous and often wrong base pairing. E. UV-light-induced thymine dimers Ultraviolet irradiation at 260 nm wavelength induces covalent bonds between adjacent thymine residues at carbon positions 5 and 6. If located within a gene, this will interfere with replication and transcription unless repaired. Another important type of UV-induced change is a photoproduct consisting of a covalent bond between the carbons in positions 4 and 6 of two adjacent nucleotides, the 4–6 photoproduct.