About the DNA Replication Simulator
This animated simulator shows a single replication fork copying an 80-base-pair stretch of double-stranded DNA. Helicase unwinds the helix and exposes the two template strands, then DNA polymerase III reads each template (3'→5') and adds the Watson-Crick complement (A–T, G–C) to build a new 5'→3' strand. The result is semi-conservative: every daughter helix keeps one original strand and one newly made strand.
The leading strand grows continuously toward the moving fork, while the lagging strand is built backwards as short Okazaki fragments (10 bp each), every fragment opened by an RNA primer from primase and later joined by ligase. The Controls let you set replication speed (0.5×–5×), adjust zoom, toggle molecule labels and base pairs, and Play, Reset or single-Step the fork. The live panel tracks bases replicated, percentage complete, Okazaki count and the current stage.
Frequently Asked Questions
What does this simulation actually show?
It animates one replication fork copying an 80-base-pair DNA segment in real time. You watch helicase split the double helix, polymerase build the leading and lagging strands, primase lay RNA primers, and ligase seal the fragments, with running statistics for bases replicated, percentage done and Okazaki fragment count.
What does semi-conservative replication mean?
It means each new double helix contains one parental (template) strand and one freshly synthesised strand, rather than two entirely new strands. The simulator reflects this: the original template stays in place while a complementary new strand is added beside it, producing two identical helices that each retain half of the original.
Why is there a leading strand and a lagging strand?
DNA polymerase can only add nucleotides in the 5'→3' direction, but the two template strands run antiparallel. One new strand (leading) can follow the fork continuously, while the other (lagging) must be made in short pieces pointing away from the fork. The simulation draws the leading strand as one line and the lagging strand as separate fragments.
What do the speed and zoom controls do?
Replication speed multiplies how far the fork advances each animation frame, from 0.5× up to 5×, so you can slow the process down to inspect each enzyme or speed it up to see the whole copy finish. Zoom (0.5×–2.5×) scales the base-pair spacing on the canvas; base letters only appear once each base is wide enough to read.
What are Okazaki fragments?
Okazaki fragments are the short stretches of new DNA that make up the lagging strand. Because the lagging template runs the "wrong" way for the fork, polymerase repeatedly starts a new fragment behind the fork and extends backwards. In this model each fragment is 10 base pairs, begins with an RNA primer, and is later stitched to its neighbour by ligase.
What does each enzyme in the legend do?
Helicase (yellow) unwinds the helix at the fork by breaking the hydrogen bonds between base pairs. Primase (red) lays the short RNA primer that polymerase needs to begin. DNA polymerase III (green) extends both new strands. Ligase (purple) seals the nicks between completed Okazaki fragments so the lagging strand becomes continuous.
How are the new base pairs decided?
Each new nucleotide is the Watson-Crick complement of the template base it pairs with: adenine pairs with thymine and guanine pairs with cytosine. The simulator stores a fixed complement map and reads the random template sequence base by base, so the new strand is always an exact complementary copy, just like in a living cell.
Is this physically accurate?
It is a faithful conceptual model rather than a molecular-dynamics simulation. The order of events, the antiparallel directionality, semi-conservative copying, RNA priming and ligation are all correct. The numbers are scaled for clarity: real Okazaki fragments are roughly 100–200 bases in eukaryotes and 1,000–2,000 in bacteria, and many other proteins (clamp, topoisomerase, single-strand binding proteins) are omitted.
How fast and accurate is real DNA replication?
In bacteria, polymerase adds around 1,000 nucleotides per second, while human cells copy roughly three billion base pairs in about eight hours using thousands of replication origins at once. Fidelity is extraordinary: base selection plus proofreading and mismatch repair leave an error rate near one mistake per billion bases copied.
Why does DNA replication matter in real life?
Accurate replication underpins cell division, growth and inheritance, so faults in it drive mutations, ageing and cancer. The enzymes shown here are also biotechnology tools: DNA polymerases power PCR and DNA sequencing, ligases join fragments in cloning, and replication inhibitors are used as antibiotics and chemotherapy agents.