Simulation viewer
A twelve-helix DNA origami sheet, as the simulator sees it. Turn it, watch it move at room temperature, and step through the anneal to see where each staple binds.
The relaxed shape from the base-pair elastic model. This sheet is laid out at 10.67 base pairs per turn, looser than DNA prefers, so it winds up along its length.
Each staple is colored by the melting temperature of its strongest domain, from 30 °C or below to 65 °C or above.
Brownian dynamics of the elastic model in water at 25 °C. Real fluctuations are a few ångströms, so the view exaggerates them and smooths out the fastest jitter.
One simulated anneal from 80 to 25 °C. Staples appear as their domains bind the scaffold. They are drawn on the final shape, since the folding model tracks binding, not position.
- Predicted yield
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- Folding midpoint
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- Size
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- Twist
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These are model predictions. The folding temperature model matches one published measurement but has not yet been calibrated against our own lab data.
What you are looking at
Each sphere is one nucleotide, placed from the base-pair frames of the relaxed elastic model the same way the simulator prepares a starting configuration for oxDNA. Strands run as tubes from their 5′ to their 3′ end. The scaffold is the long gray strand; the colored strands are staples.
Motion shows 20 nanoseconds of overdamped Brownian dynamics of the same elastic model. It shows which parts are floppy and which are stiff, not rare events such as a staple letting go.
Folding replays a single stochastic trajectory of the domain-level model under the standard protocol: 80 °C, cooling by 1 °C a minute to 65 °C, then 10 minutes a degree to 25 °C. Another run would bind staples in a slightly different order. The yield figure comes from many such runs.