toeholdmediated

Toehold-mediated strand displacement is a mechanism by which a single-stranded DNA fragment, called the invader, binds to a complementary single-stranded overhang (the toehold) on a double-stranded DNA complex and displaces one of the strands via branch migration. The toehold provides an initial binding site and dictates specificity and kinetics. After initial binding, branch migration—random, sequential base-pair exchange along the duplex—propagates until the incumbent strand is fully displaced, yielding a new duplex consisting of the invader strand bound to the formerly complementary strand.

Kinetics: Toehold length and sequence strongly influence the rate. Longer toeholds (roughly 5–8 nucleotides, up to 12) accelerate initiation; the rate slows with weaker bindings or with obstructed toeholds. The process is thermodynamically favorable when the invading duplex forms a more stable duplex than the displaced arrangement; non-equilibrium conditions can bias direction.

Design considerations: Toehold design controls leak (undesired displacement without intended invader), orthogonality (different toehold sequences do not cross-react), and unwanted secondary structures. In practice, systems use cascaded or competitive displacement to implement logic operations, dynamic assemblies, and signal amplification.

Applications: Toehold-mediated strand displacement underpins DNA strand-displacement circuits, molecular computation, biosensors, programmable self-assembly, and dynamic DNA nanostructures. Variants include multi-step cascades, catalytic circuits where a single invader triggers multiple rounds, and toehold exchange reactions for reversible reconfiguration.