DNA replication: the replication fork !

To copy DNA the double helix opens into a fork: one strand is copied continuously and the other in pieces (Okazaki fragments).

Updated 2026-11-01

Key facts

Semiconservative: each daughter molecule keeps one old strand and one new strand.
DNA polymerase only extends 5'→3' and needs a primer with a free 3'-OH (laid down by primase, made of RNA).
Leading strand: continuous. Lagging strand: discontinuous, in Okazaki fragments that are joined later.
In eukaryotes: pol α-primase starts, pol ε extends the leading strand, pol δ the lagging strand; PCNA is the sliding clamp.
Many replication origins per chromosome in eukaryotes; a single one (oriC) on the bacterial chromosome.

1. Licensing (G1 phase): ORC marks the origins and loads the MCM2-7 helicase in an inactive form, so each origin fires only once per cycle.
2. Opening (S phase): CDK and DDK kinases activate the CMG helicase (Cdc45-MCM-GINS), which separates the strands using ATP.
3. Single-strand binding proteins (RPA in humans, SSB in bacteria) stop the strands from re-pairing.
4. Positive supercoiling builds up ahead of the fork: topoisomerases I and II (gyrase in bacteria) relieve it.
5. Primase lays down a short RNA primer; RFC loads PCNA and polymerase δ or ε extends from the 3'-OH.
6. On the lagging strand, FEN1 and RNase H remove the primers, pol δ fills the gap and DNA ligase I seals the nick (uses ATP; NAD⁺ in bacteria).
7. Fidelity: base selection, the 3'→5' proofreading exonuclease and mismatch repair bring the error rate to about 1 in 10⁹ bases.
8. At the ends of linear chromosomes a gap is left on the lagging strand: telomeres shorten with every division unless telomerase acts.

Order at the fork: 'Hello, Tiny Primer, Please Ligate' = helicase, topoisomerase, primase, polymerase, ligase.

Fluoroquinolones target bacterial gyrase and topoisomerase IV; camptothecins and etoposide target human topoisomerases in chemotherapy.
Nucleoside analogues (cytarabine, gemcitabine, aciclovir) terminate or stall the chain once the polymerase incorporates them.
Defects in RecQ helicases cause genome-instability syndromes (Bloom, Werner).

Think of the answer, then tap the question to see it.

Why is one strand replicated in pieces?

Polymerase only works 5'→3'; the lagging strand runs opposite to fork movement and is copied as Okazaki fragments.

Which enzyme seals Okazaki fragments, and what does it use in humans?

DNA ligase I; it forms the last phosphodiester bond using ATP.

Which protein is the sliding clamp for polymerase δ?

PCNA, a ring around the DNA that keeps the polymerase on (processivity); RFC loads it.

What stops a eukaryotic origin from firing twice in one cycle?

MCM helicase is only loaded (licensed) in G1; in S phase CDKs activate it and also block new loading.

Educational information, not medical advice. For any symptom, see a health professional.

Sources: DNA Replication (Reactome, 2026); DNA strand elongation (Reactome, 2026); POLD1: DNA polymerase delta catalytic subunit (human) (UniProt, 2026); Textbook of Biochemistry for Medical Students, 6th ed. (Jaypee Brothers Medical Publishers (Vasudevan DM, Sreekumari S, Vaidyanathan K), 2011).

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Representative model, for educational purposes only.