Overall, the error rate in replication is less than one mistake per billion nucleotides. How is this incredible accuracy achieved?
DNA polymerases are very particular in pairing nucleotides with their complements on the template strand. Errors in nucleotide selection by DNA polymerase arise only about once per 100,000 nucleotides. Most of the errors that do arise in nucleotide selection are corrected in a second process called proofreading. When a DNA polymerase inserts an incorrect nucleotide into the growing strand, the 3′-OH group of the mispaired nucleotide is not correctly positioned in the active site of the DNA polymerase for accepting the next nucleotide. The incorrect positioning stalls the polymerization 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 1 in 10 million nucleotides.
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A third process, called mismatch repair (considered further in Chapter 13), corrects errors after replication is complete. Any incorrectly paired nucleotides remaining after replication produce a deformity in the secondary structure of the DNA; that deformity is recognized by enzymes that excise the incorrectly paired nucleotide and use the original nucleotide strand as a template to replace the incorrect nucleotide.
Replication is extremely accurate, with less than one error per billion nucleotides. The high level of accuracy in DNA replication is produced by nucleotide selection, proofreading, and mismatch repair, each of which catches errors missed by the preceding processes.
The Basic Rules of Replication
Bacterial replication requires a number of enzymes (see Table 9.3), proteins, and DNA sequences that function together to synthesize a new DNA molecule. These components are important, but we must not become so immersed in the details of the process that we lose sight of the general principles of replication:
Replication is always semiconservative.
Replication begins at sequences called origins.
DNA synthesis begins with the synthesis of short segments of RNA called primers.
The elongation of DNA strands is always in the 5′→3′ direction.
New DNA is synthesized from dNTPs; in the polymerization of DNA, two phosphate groups are cleaved from a dNTP and the resulting nucleotide is added to the 3′-OH group of the growing nucleotide strand.
Replication is continuous on the leading strand and discontinuous on the lagging strand.
New nucleotide strands are complementary and antiparallel to their template strands.
Replication takes place at very high rates and is astonishingly accurate, thanks to precise nucleotide selection, proofreading, and mismatch repair.