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DNA Replication Simulator

DNA molecule · 30 base pairs Fork 0/18 Leading 0/19 Lagging 0/14 Nicks – Supercoiled

5′Top

3′Top

3′Btm

5′Btm

Select a tool to begin!

Enzyme rack — tap to apply

Free nucleotide pool

Focus Drop here

Strand base –

Required partner

Need: —

Two rings = purine (A, G), one ring = pyrimidine (T, C).

DNA Replication Simulator

One 30 base-pair molecule, five enzymes, two new strands built by you.

Unzip the molecule at a replication fork.
Match every new base to the strand below.
Seal the gaps, then read your run log.

1 · Antiparallel strands

The two strands run opposite ways

Left to right, the top strand reads 5′→3′. Left to right, the bottom strand reads 3′→5′.

That one fact is why the two new strands get built so differently.

2 · Base pairing

A–T is two bonds, G–C is three

A always pairs with T, held by two hydrogen bonds. G always pairs with C, held by three.

Wide tiles are two-ring bases (A, G); narrow tiles are one-ring bases (T, C).

3 · Leading and lagging

One piece, or many

New DNA only grows 5′→3′. On one strand that points toward the fork, so it runs as one continuous piece.

On the other it points away. Polymerase keeps restarting, giving short Okazaki fragments.

4 · The enzymes, in order

Topoisomerase — relieves twisting strain ahead of the fork.
Helicase — breaks the hydrogen bonds and opens the fork.
Primase — lays a short RNA primer to start from.

5 · The enzymes, in order

DNA polymerase — adds each matching nucleotide, 5′→3′ only.
Ligase — seals the gaps left between the fragments.

Apply the wrong one and the plate tells you which one it wanted.

Assumptions · what it gets right

Each new double helix keeps one old strand.
Strands are antiparallel; new DNA is only added 5′→3′.
That forces one continuous strand and one of fragments.
A–T is two hydrogen bonds, G–C is three.

Exaggerated on purpose

30 base pairs, and the fork opens 18. A real chromosome is hundreds of millions of pairs. You could never check one pairing at that scale.
Three Okazaki fragments of 4, 4 and 6 bases. Real fragments are 100–200 nucleotides. Short ones make the discontinuity countable.

Exaggerated on purpose

One base is added per student action. Real polymerase adds about 50 bases a second. The pace here is the teaching, not the rate.
The enzymes act one at a time, in strict order. In the cell they work together in a replisome. Separating them is what makes each job nameable.

What it leaves out

Single-strand binding proteins, the sliding clamp and the clamp loader.
Proofreading and mismatch repair — this model just refuses a wrong base.
The second fork: a real origin opens a bubble with two.

What it leaves out

RNA primer removal, folded into the ligase step here.
Telomeres and the end-replication problem.

You can be asked to evaluate a model, so these choices are worth knowing.

Replication run log

DNA Replication Simulator · Specimen: 30 base pairs

Enzyme order applied—

Bases placed0 of 33

First-try accuracy—

Leading strand0 of 19

Lagging strand0 of 14

Nicks3 → 0

Read the readout The NICKS counter went from 3 to 0 in a single step. Which enzyme changed it, and what kind of bond did it form between the fragments?

1. Topoisomerase — Relaxes supercoiled DNA by cutting and rejoining strands, relieving tension ahead of the replication fork.
2. Helicase — Unwinds the DNA double helix by breaking hydrogen bonds between base pairs, separating the two strands.
3. Primase — Synthesizes short RNA primers that provide a 3′-OH starting point for DNA polymerase to begin synthesis.
4. DNA polymerase — Adds complementary nucleotides to the exposed strands in the 5′ to 3′ direction, proofreading as it goes.
5. Ligase — Joins Okazaki fragments on the lagging strand by forming phosphodiester bonds between adjacent nucleotides.