A DNA walker is not powered by ATP like a protein motor — it is powered by base-pairing energy released through toehold-mediated strand displacement. The track is a line of single-stranded DNA "anchor" strands. Each of the walker's two legs is a short strand partially complementary to an anchor; a leg binds by first latching onto a short unpaired "toehold" overhang, then zips further in, displacing whatever was there and locking the leg down. The trailing leg is released — usually by a competing "fuel" strand that hybridizes with the anchor it just left more completely than the leg did — freeing it to swing forward, past the other leg, to the next unclaimed anchor. Repeating this hand-over-hand cycle drags the whole walker along the track.
trailing leg detaches from anchor[i]
if (ratchet) anchor[i] -> burnt (irreversible)
trailing leg binds anchor[i±1 beyond leading leg]
roles swap: trailing ↔ leading
- Burnt-bridge ratchet — when on, each vacated anchor is chemically consumed (its strand is cut or the toehold destroyed) so a leg can never rebind behind itself; this one-way constraint is what turns random thermal fluctuation into net directional travel. Switch it off and the walker has no preferred direction — it steps forward or backward with equal odds, a pure random walk with zero average progress.
- Fuel / toehold concentration — higher concentration of the strand-displacement trigger speeds up how fast a leg can be released and rebind, shortening the pause between steps.
- Anchor spacing — the distance each leg must reach to bind the next site; real DNA-origami tracks pattern anchors at ~2–7 nm, matched to the ~7 nm reach of a two-domain leg.
- Processivity — the fraction of steps that land forward rather than backward; a good burnt-bridge walker is close to 100% processive, while an unratcheted one hovers near 50%.
Real-world relevance: burnt-bridge DNA walkers (Sherman & Seeman's original design, and later cargo-sorting variants) are used to autonomously ferry nanoparticles, transport cargo between reaction sites, or execute programmed sequences of pickup-and-drop steps on a DNA origami breadboard — a mechanical algorithm made entirely of base-pairing chemistry.