Chromatin Structure Simulator (2D)

Packing level

Zoom level 1 — Double helix

Helix Nucleosomes 30nm fibril Chromosome

Linker DNA length 40 bp

Sets nucleosome repeat length (core 147 bp + linker). Longer linkers mean more DNA per bead, so the beads-on-a-string state compacts less.

Chromatin state

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

Readout

Packing level

Bare DNA double helix

Nucleosome repeat length

187 bp

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. This 2D diagram morphs a schematic strand through four textbook levels of that hierarchy, each built from the level below it, viewed edge-on so the coiling reads as a flattened spring.

Level 1 — naked double helix: ~2 nm diameter, 1× (reference length)
Level 2 — nucleosomes: 147 bp core + linker DNA wrapped around a
           histone octamer every (147+linker) bp -> ratio = repeat_bp x 0.34nm / 11nm bead
Level 3 — 30-nm fibril: nucleosomes coil into a solenoid,
           roughly 6x tighter than the beaded chain
Level 4 — mitotic chromosome: looped and supercoiled onto a
           scaffold, roughly 250x tighter again

Zoom level — scrubs through the four packing levels.
Linker DNA length — the real variable that sets how much DNA each nucleosome "uses up"; it drives the compaction ratio shown at level 2 directly from the formula above.
Euchromatin — loosely packed chromatin (levels 3-4 spread out). 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.

This is a schematic teaching diagram, not a molecular-dynamics simulation — bead layout and coil radii are chosen for legibility on a flat canvas, while the compaction numbers are derived from the nucleosome-repeat-length formula and commonly cited textbook multipliers for the higher packing levels.

Histone octamer DNA strand Marked gene locus

Marked geneACCESSIBLE