A nanofactory you can actually build
DNA origami is the most reproduced result in molecular nanotechnology: a single ~7 kb scaffold strand folded by ~200 short “staple” oligos self-assembles into an arbitrary nanoscale shape, in a single heat-and-cool pot. Molecular Synth turns that into a one-command pipeline + a desktop rig.
Rig from orderable parts
Repurposed Peltier thermocycler, DIY gel, optional DIY STM — all linked & priced.
Atomic-precision output
Sequence-addressed nanostructures, ~3 nm feature fidelity; ~10¹² copies per reaction.
Shape → recipe
STL/PLY/preset → scaffold + optimized staples + protocol + a 3D oxDNA structure.
Proofs pass
Independent-tool Tm, valid oxDNA structure, simulated control loop, power & fluidics.
How a request becomes matter
shape → A-trail scaffold routing → staple-break yield optimizer (Tm balance · loop-closure · off-target · cross-dimer) → order oligos → fold (90→20 °C in Mg²⁺) → gel-verify → optional silica hardening
What it makes — today
Atomic-precision DNA-origami nanostructures: any shape you describe, folded from a scaffold + optimized staples, in ~10¹² copies per reaction. Everything above this rung is honestly labelled on the vision tab.
🧬 Shapes
Platonic presets, or any STL/PLY/JSON wireframe → a single closed scaffold route + optimized staple set + the wet-lab protocol + a relaxable 3D oxDNA structure.
🔬 Functionalised
Rung-2: handle staples position enzymes / catalysts / nanoparticles at nm-precise sites; cascade placement at a target inter-guest spacing.
🪨 Hardened
Optional sol–gel silica converts the floppy DNA into a rigid SiO₂ replica — a real rung toward durable inorganic nanostructures.
The honest line
The output is a DNA-self-assembled nanostructure (~10 nm–1 µm), not a macroscopic object and not Drexler diamondoid mechanosynthesis. Every capability cites a demonstrated paper; the bigger “matter compiler” ambition stays clearly on the north-star track. We climb one tested rung at a time.
Blueprint — every part, with links & prices
Live from the repo’s single-source bom.json (the same file the validate gate checks). Rig hardware is the one-time build; consumables are per design.
Build it — the phases
Full step-by-step (wiring, gel conditions, the rig-validation-first discipline) in the build guide, and the system integration (power, thermal, fluidics, safety) in integration.md.
The synthesizer thesis — what’s real, what’s north-star
“Ask for anything, a machine makes it.” A universal replicator isn’t possible today, any price. But the spirit is partly real now — and there’s a real research staircase from DNA toward programmable molecular manufacturing, every rung demonstrated in a lab.
| You ask for… | Today? | How |
|---|---|---|
| A nanostructure (atomic precision) | ✓ ready | this repo (DNA origami) |
| A functionalised / hardened nanostructure | ✓ ready | handle staples; sol–gel silica |
| A custom enzyme / molecule | 🔬 frontier | directed evolution, DNA-templated synthesis |
| Carbon → oxygen / a working phone | ⭐ north-star | nuclear / fabs — not buildable |
The ladder
DNA origami → breadboard → DNA-templated synthesis → robots → assemblers → general manufacturing. the-ladder.md
“CRISPR for molecules?”
Element change is a nuclear wall; molecule building is real chemistry; the tool is engineered enzymes/assemblers. molecule-vs-element.md
Why it’s real
A citation per claim, mechanically gated. science.md