3D viewer
Designs from our simulator, in 3D. Each one is DNA folded into a shape a few tens of nanometres across. Turn it, watch it move in water, and watch it fold as the mix cools.
Positioner
A DNA machine about 40 nm long, built from 24 DNA double helices packed side by side. It holds molecule A right next to molecule B so the two can react, and holds a third molecule, C, far away as a control.
The shape the simulator predicts once it has folded.
How it moves in water at room temperature. How far each part moves is the prediction. How fast is not, because the model’s water drags too much. Real movements are a few tenths of a nanometre, so the view exaggerates them.
In the lab, the strands are mixed and cooled slowly from 80 to 25 °C, and each staple finds its place on the scaffold as the mix cools. This replays one simulated run, drawn on the finished shape. A, B and C are added after folding, so they appear at the end.
- Tube One DNA double helix, 2 nm across
- Bead One nucleotide, a single letter of DNA
- Gray The scaffold, one long DNA strand that runs through every helix
- Colors Staples, short strands that pin the scaffold into shape, one color each
- Colors How firmly each staple holds on. The model predicts that weak ones (orange) let go near 30 °C and strong ones (teal) hold past 65 °C
- Balls The molecules A, B and C, each held on a short DNA handle
Reactants
- Every staple in place
- –
- Folding temperature
- –
- Twist
- –
- Size
- –
These are model predictions, not yet calibrated against our own lab data. Read the staple count as an upper bound: the model assumes every staple is made perfectly and binds as well at the edges as in the middle. Measured on real origami, staple incorporation averages about 84 percent per site and 48 percent at the edges (Strauss et al. 2018, doi.org). The folding temperature has been compared with one published measurement, on a flat sheet. For a 3D block like this one it is probably too high, likely by 10 to 20 °C: the model has no electrostatic cost for packing helices together, and published 24-helix bundles fold between about 68 and 48 °C.
What you are looking at
DNA origami folds one long DNA strand, the scaffold, into a chosen shape. A few dozen to a few hundred short strands, the staples, each pair with the scaffold in one or more places, and a staple that pairs with stretches from different parts of the scaffold pulls them together. Mixed in salty water and cooled slowly, they assemble themselves. The shapes here are a few tens of nanometres across, more than a thousand times thinner than a hair.
Helices draws each DNA double helix as a tube 2 nm across, its real width, colored by the staple bound in it. Gray is the scaffold, which runs through every tube; where no staple has bound yet it shows as a thin gray strand. The short links between tubes are crossovers, where a strand hops from one helix to the next. Nucleotides draws every base instead: a bead for each nucleotide along both strands and a rung across each base pair. The shape comes from the simulator’s elastic model of DNA.
The positioner is our first DNA machine. It carries each reactive molecule on a handle, a short single strand added to one staple. The molecule rides on a matching short strand that pairs with the handle, and is added after folding. The colored ball marks where it attaches, the faint shell around it shows how far the model predicts it wobbles at 25 °C, and the white rod is the handle, drawn straight out although in water it swivels. The distances and effective concentrations are predictions of the model and have not been measured yet.
Motion shows the same model jostled by water, a Brownian dynamics simulation. It shows which parts are floppy and which are stiff, not rare events such as a staple letting go.
Folding replays one simulated run of our standard cooling: 5 minutes at 80 °C, then 1 °C a minute down to 65 °C, then 10 minutes a degree down to 25 °C. Another run would place the staples in a slightly different order. The count of runs that end with every staple in place comes from 16 such runs.