Mismatch Repair

Replication is extremely accurate: each new copy of DNA has only one error per billion nucleotides. However, in the process of replication, mismatched bases are incorporated

Table 17.5 Summary of common DNA repair

mechanisms

Repair System

Type of Damage Repaired

Mismatch

Replication errors, including mispaired bases and strand slippage

Direct

Pyrimidine dimers; other specific types of alterations

Base-excision

Abnormal bases, modified bases, and pyrimidine dimers

Nucleotide-excision

DNA damage that distorts the double helix, including abnormal bases, modified bases, and pyrimidine dimers

into the new DNA with a frequency of about 10~4 to 10~5; so most of the errors that initially arise are corrected and never become permanent mutations. Some of these corrections are made in proofreading (see p. 000 in Chapter 12). DNA polymerases have the capacity to recognize and correct mismatched nucleotides. When a mismatched nucleotide is added to a newly synthesized DNA strand, the polymerase stalls. It then uses its 3': 5' exonuclease activity to back up and remove the incorrectly inserted nucleotide before continuing with 5': 3' polymerization.

Many incorrectly inserted nucleotides that escape detection by proofreading are corrected by mismatch repair (see p. 000 in Chapter 12). Incorrectly paired bases distort the three-dimensional structure of DNA, and mismatch-repair enzymes detect these distortions. In addition to detecting incorrectly paired bases, the mismatch-repair system corrects small unpaired loops in the DNA, such as those caused by strand slippage in replication (see Figure 17.14). Some trinucleotide repeats may form secondary structures on the unpaired strand (see Figure 17.6d), allowing them to escape detection by the mismatch-repair system.

After the incorporation error has been recognized, mismatch-repair enzymes cut out the distorted section of the newly synthesized strand and fill the gap with new nucleotides, by using the original DNA strand as a template. For this strategy to work, mismatch repair must have some way of distinguishing between the old and the new strands of the DNA so that the incorporation error, and not part of the original strand, is removed.

The proteins that carry out mismatch repair in E. coli differentiate between old and new strands by the presence of methyl groups on special sequences of the old strand. After replication, adenine nucleotides in the sequence GATC are methylated by an enzyme called Dam methylase. The process of methylation is delayed and so, immediately after replication, the old strand is methylated and the new

New DNA

ffi In DNA replication, a mismatched base was added to the new strand.

^a Methylation at GATC sequences allows old and newly synthesized nucleotide strands to be differentiated: immediately after replication, the old strand will be methylated but the new strand will not.

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