Chromatin Structure Simulator

Packing level

Zoom level 1 — Double helix

Helix Nucleosomes 30nm fibril Chromosome

Chromatin state

Open, decondensed — genes are exposed to the transcription machinery.

Readout

Packing level

Bare DNA double helix

Compaction vs. naked DNA

1× (baseline)

Gene accessibility

ACCESSIBLE

How it works

Two metres of DNA fit inside a nucleus a few micrometres across because it is folded hierarchically rather than crumpled randomly. Each fold level trades reach — how far a protein has to travel to find a gene — for compactness. The slider morphs the same simulated DNA strand through four textbook levels of that hierarchy, each one built from the level below it.

Level 1 — naked double helix: ~2 nm diameter, 1× (reference length)
Level 2 — nucleosomes: 147 bp wrapped ~1.65 turns around a histone
           octamer (2×H2A·H2B·H3·H4) every ~200 bp → ~6-7× shorter
Level 3 — 30-nm fibril: nucleosomes coil into a solenoid,
           stabilised by linker histone H1 → ~40× shorter
Level 4 — mitotic chromosome: looped and supercoiled onto a
           scaffold → ~10,000× shorter than naked DNA

Zoom level — scrubs through the four packing levels; histone-octamer beads fade in as level 1 gives way to level 2, then the same beads re-arrange into a tighter coil at each higher level.
Euchromatin — loosely packed chromatin (lower levels 3-4 spread out, more space between coils). RNA polymerase and transcription factors can reach the DNA, so the marked gene reads accessible.
Heterochromatin — densely packed chromatin (levels 3-4 pull tight). The same gene is buried inside the coil and reads blocked — this is how cells silence genes without changing the DNA sequence itself (epigenetic regulation).

The 3D geometry here is a schematic teaching model, not a molecular-dynamics simulation — bead counts and coil radii are chosen for legibility, while the compaction numbers quoted in the readout panel reflect commonly cited textbook figures for each packing level.

Histone octamer DNA strand Marked gene locus

Marked geneACCESSIBLE

⚠ Couldn't load the 3D engineThree.js failed to load from the CDN. Check your connection and reload.