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PolskiDNA Replication Fork: Leading Strand, Lagging Strand & Okazaki Fragments (2D)
A real replication-fork process diagram: helicase unwinds the duplex at an adjustable bp/s rate, leading-strand polymerase synthesizes continuously in the 5'→3' direction, and lagging-strand polymerase builds discontinuous Okazaki fragments — primed by primase, extended backward, and sealed by ligase — with real A-T/G-C base pairing on every nucleotide added.
About this replication-fork simulation
The 3D companion shows a double helix visually unzipping as a decorative traveling wave — a good sense of shape, but it does not model the machinery that actually does the unzipping and copying. This 2D companion drives the real replication-fork process instead: a helicase enzyme, drawn as the "H" marker, unwinds the parental duplex at the rate set by the helicase slider (bp/s), exposing single-stranded template on both sides of the fork for the two polymerases to read.
Because DNA polymerase can only extend a new strand in the 5'→3' direction, the two exposed templates cannot be copied the same way. The leading strand is synthesized continuously, following the fork as it opens — set its polymerase speed below the helicase rate and you can watch a real gap of exposed single-stranded template open up between the polymerase and the fork, exactly as happens when replication machinery is unbalanced in a real cell. The lagging strand's template runs the wrong way for continuous synthesis, so primase lays a short RNA primer (orange) every "Okazaki fragment length" bases behind the fork, and polymerase extends each primer backward until it reaches the previous fragment; DNA ligase then seals the nick, and the fragment turns from green (growing) to teal (ligated). Every nucleotide added to either new strand is chosen by the real Watson–Crick rule against its template base, A always with T and G always with C, and colored consistently across both strands.
Frequently Asked Questions
How is this different from the 3D "DNA Replication: A Molecular Animation"?
The 3D version animates a single traveling "unzip wave" along a fixed decorative helix geometry — it looks like replication but does not model helicase rate, polymerase speed, or the leading/lagging strand asymmetry. This 2D companion simulates the actual replication-fork mechanism: an adjustable helicase unwind rate, independently adjustable leading- and lagging-strand polymerase speeds, and a real Okazaki-fragment/primase/ligase cycle on the lagging strand.
Why is the lagging strand made in fragments instead of one continuous piece?
DNA polymerase can only add nucleotides in the 5'→3' direction. On the leading-strand template that direction happens to match the direction the fork is opening, so synthesis is continuous. On the lagging-strand template it does not — polymerase would have to run away from the fork, so instead primase repeatedly lays short RNA primers close to the fork, and polymerase extends each one backward (toward the previous fragment) in short bursts called Okazaki fragments, which ligase then joins into a continuous strand.
What happens if I set the leading-strand polymerase slower than helicase?
The fork keeps unwinding at the helicase rate regardless of how fast either polymerase is working, so a slow leading-strand polymerase falls behind and a real stretch of exposed single-stranded template (ssDNA) opens up between the polymerase and the fork — tracked live in the "Leading ssDNA gap" readout. In real cells this gap is coated by single-strand binding proteins to keep it stable until polymerase catches up.
Replication-fork process sim with an adjustable helicase unwind rate, independent leading- and lagging-strand polymerase speeds, a real primase/Okazaki-fragment/ligase cycle, and Watson–Crick base pairing on every synthesized nucleotide.
2D · HTML5 Canvas 2D · 60 FPS target · runs fully client-side, no install