DNA Structure Simulator — GC base pairs, AT base pairs & Hydrogen bonds Interactive

Explore an antiparallel double helix with two sugar-phosphate backbones, complementary base pairs and grooves.

← Biology Labs
About this tool — how it works & FAQ

About the DNA Structure Simulator

Explore an antiparallel double helix with two sugar-phosphate backbones, complementary base pairs and grooves. Change GC content and helical twist, then open the base pairs to inspect hydrogen bonding.

What the simulator shows

• 3D scene parts: Strand 1 sugar-phosphate backbone; strand 2 sugar-phosphate backbone; complementary base pairs; major and minor groove guide. • Controls: Displayed base-pair count (10–30 bp); GC fraction (0–1 fraction); Helical turn size (9–12 bp/turn); Separate base pairs (0–1 illustrative). • Live readouts: GC base pairs (bp); AT base pairs (bp); Hydrogen bonds; Displayed helix turns. • Guided experiments: All AT; All GC. • Four tabs (visual laboratory, curves and measurements, experiments, learn and assess), a model-verification run, a timestamped event log and a trial report.

The model equations

GC pairs = round(N·GCfraction) AT pairs = N − GC pairs Hydrogen bonds = 3·GC pairs + 2·AT pairs Turns = N / (bp per turn)

Model limits and how to explore

Molecular geometry, organelle dimensions and animation time are enlarged and illustrative. Colors identify structures rather than natural tissue color. This is a conceptual teaching model, not a cell physiology predictor. Base counts are exact for the displayed representative sequence. Twist is user-controlled, not a thermodynamic or melting calculation. Try the preset experiments, then compare the live readouts with the equations.

Frequently asked questions

Does the animation show literal molecular dimensions and timing?

No. Geometry is enlarged and time is a teaching playback scale.

How many hydrogen bonds are in a GC base pair?

Three.

What does this simulator not model?

Molecular geometry, organelle dimensions and animation time are enlarged and illustrative. Colors identify structures rather than natural tissue color. This is a conceptual teaching model, not a cell physiology predictor. Base counts are exact for the displayed representative sequence. Twist is user-controlled, not a thermodynamic or melting calculation.

Related tools & guides