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Grades 9–12 · Organisms

How can DNA polymerase remove a copying mistake?

DNA copying is highly accurate without being perfect. A DNA polymerase builds a new strand using an existing strand as a template. It adds nucleotides, the building units containing a base, sugar and phosphate, to the growing strand’s three-prime end, conventionally written 3′.

O51 visual explanationTemplate C; new terminal base G. G restores complementary pairing. The complete before-and-after diagram separates the erroneous A from the corrected G; controls emphasize parts of that sequence.Proofreading edits the newly made strand▸ Before: A mismatches CAfter: G pairs with CTemplate3′5′5′3′New strandTAATCTemplate3′5′5′3′New strandTAATCAGSynthesis siteEditing siteAEnd returnsARemovedThe template guides complementary addition.

In the diagramProofreading edits the newly made strand▸ Before: A mismatches CAfter: G pairs with CTemplate3′5′New strandTACGSynthesis siteEditing siteEnd returnsRemovedThe template guides complementary addition.

The growing strand’s end can move between synthesis and editing sites. In this example, an incorrect A opposite C is removed and a G is added.

Base pairing helps select the next nucleotide: A normally pairs with T, and C with G. Occasionally, however, an incorrect nucleotide is incorporated. A mismatch at the new strand’s end can fit poorly and slow further extension. In a proofreading polymerase system, that end can enter a separate editing active site rather than immediately accepting another nucleotide.

The editing activity is a 3′-to-5′ exonuclease. It hydrolyzes a bond in the newly made strand and removes a nucleotide from its end. Removing the mismatched terminal unit can restore a correctly paired end with the chemical group needed for further synthesis. The strand can then return to the polymerizing site, where addition proceeds again in the 5′-to-3′ direction.

The illustration isolates one mistake opposite a template C: an incorrect A is removed before a G is added. It does not show the template being rewritten to match the error. Proofreading lowers the chance that an error persists, but it cannot guarantee error-free copying. Not all polymerases have their own proofreading activity, and other repair systems can handle some mismatches that escape the copying machinery.

About this explanation

Starting knowledge: Understands DNA base pairing, enzymes and that a nucleotide belongs to a directionally organized strand.

Sources

  • Freemont and colleagues, PNAS — Cocrystal structure of an editing complex of Klenow fragment with DNA
  • Beese and Steitz, EMBO Journal — Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I
  • Alberts and colleagues, Molecular Biology of the Cell, NCBI Bookshelf — DNA Replication Mechanisms
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