Mechanism of DNA Replication

Replication of DNA

• Replication begins at a specific sequence called the Origin of Replication (ori).​
• A replicon is the unit of DNA that replicates from a single origin.​
• Helicase binds at ori and unwinds the double helix by breaking hydrogen bonds between bases.​
• This creates a replication fork - a Y-shaped structure where synthesis occurs.​
• Topoisomerase (DNA Gyrase) acts just ahead of helicase to relieve torsional stress and prevent supercoiling.​
• SSBPs coat the separated single strands to keep them open and prevent reannealing.​

• DNA polymerase cannot initiate new strand synthesis on its own - it can only add nucleotides to an existing 3′-OH group.​
• Primase (a type of RNA polymerase) synthesises a short RNA primer (10–12 nucleotides) complementary to the template strand.​
• The primer provides the free 3′-OH end needed by DNA polymerase to begin adding deoxyribonucleotides.​

Leading Strand

• Synthesised continuously in the 5′→3′ direction toward the replication fork.​
• Template strand reads 3′→5′.​
• Requires only one RNA primer for the entire strand.​

Lagging Strand

• Synthesised discontinuously in the 5′→3′ direction away from the replication fork.​
• Template strand reads 5′→3′, meaning synthesis moves opposite to fork movement.​
• Short fragments called Okazaki fragments are formed, each initiated by a separate RNA primer.​

• After Okazaki fragments are synthesised, DNA Polymerase I removes the RNA primers by its 5′→3′ exonuclease activity.
• The gaps left after primer removal are filled with DNA nucleotides by DNA Polymerase I.​
• DNA Ligase then seals the remaining nicks (breaks in the phosphodiester backbone) by forming covalent bonds, joining the fragments into a continuous strand.​

1. In prokaryotes (E. coli): chromosomes are circular; replication ends when the two replication forks meet at a termination sequence (Ter site) on the opposite side of the origin.​
2. In eukaryotes: multiple replication forks travel in both directions from multiple origins and merge when adjacent replicons fuse.​

• Replication starts at the origin (ori), where helicase unwinds the helix into a replication fork, topoisomerase relieves supercoiling, and SSBPs keep the strands apart.
• Primase lays down a short RNA primer, giving DNA polymerase a free 3′-OH end to start adding nucleotides.
• The leading strand is made continuously (one primer); the lagging strand is made discontinuously as Okazaki fragments (many primers).
• DNA Pol I removes the primers and fills the gaps, and DNA ligase seals the nicks into a continuous strand.
• Termination occurs when forks meet at the Ter site (prokaryotes) or when replicons fuse (eukaryotes).