First primer Second primer
^ .the polymerase must release the template and shift to a new position farther along the template (at the third primer) to resume synthesis.
Conclusion: In this model, DNA must form a loop so that both strands can replicate simultaneously.
12.15 In one model of DNA replication in E. coli, the two units of DNA polymerase III are connected, and the lagging-strand template forms a loop so that replication can take place on the two anti-parallel DNA strands. Components of the replication machinery at the replication fork are shown at the top.
merization reaction, and the 3': 5' exonuclease activity of DNA polymerase removes the incorrectly paired nucleotide. DNA polymerase then inserts the correct nucleotide. Together, proofreading and nucleotide selection result in an error rate of only one in 10 million nucleotides.
A third process, called mismatch repair (discussed further in Chapter 17), corrects errors after replication is complete. Any incorrectly paired nucleotides remaining after replication produce a deformity in the secondary structure of the DNA; the deformity is recognized by enzymes that excise an incorrectly paired nucleotide and use the original nucleotide strand as a template to replace the incorrect nucleotide. Mismatch repair requires the ability to distinguish between the old and the new strands of DNA, because the enzymes need some way of determining which of the two incorrectly paired bases to remove. In E. coli, methyl groups (-CH3) are added to particular nucleotide sequences, but only after replication. Thus, methylation lags behind replication: so, immediately after DNA synthesis, only the old DNA strand is methylated. Therefore it can be distinguished from the newly synthesized strand, and mismatch repair takes place preferentially on the unmethylated nucleotide strand.
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