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One way the cell reduces mistakes during replication is through editing functions. With some DNA polymerases the editing function resides in the same protein, while in other cases a separate protein performs the editing function. Editing proteins are aptly named because they go back over the newly replicated DNA looking for mistakes and then recognize and remove incorrectly inserted bases (Figure 1.12). If the last nucleotide inserted in the growing DNA chain creates a mismatch, the editing function stops replication until the offending nucleotide is removed. DNA replication then continues, inserting the correct nucleotide. Because the DNA chain grows in the 5′-to-3′ direction, the last nucleotide added is at the 3′ end. The enzyme activity found in a DNA polymerase or one of its accessory proteins that removes this nucleotide is therefore called a 3′ exonuclease. The editing proteins probably recognize a mismatch because the mispairing (between T and G in the example in Figure 1.11) causes a minor distortion in the structure of the double-stranded helix of the DNA.

DNA polymerase I is an example of a DNA polymerase in which the 3′ exonuclease editing activity is part of the DNA polymerase itself. However, in DNA polymerase III, which replicates the bacterial chromosome, the editing function resides in an accessory protein encoded by a separate gene whose product travels along the DNA with the DNA polymerase during replication. In E. coli, the 3' exonuclease editing function is encoded by the dnaQ gene (Table 1.1), and dnaQ mutants, also called mutD mutants (i.e., cells with a mutation in this gene that inactivates the 3' exonuclease function), show much higher rates of spontaneous mutagenesis than do cells containing the wild-type, or normally functioning, dnaQ gene product. Because of their high spontaneous mutation rates, mutD mutants of E. coli can be used as a tool for mutagenesis, often combined with mutations in other genes whose products normally contribute to the correction of mismatches (see chapter 10).

Figure 1.12 Editing function of DNA polymerase. (A) A G is mistakenly placed opposite an A while the DNA is replicating. (B and C) The DNA polymerase stops while the G is removed and replaced by a T before replication continues.