Figure 1.

Toehold-mediated strand displacement reaction. DNA is depicted as lines with the half arrow indicating the 3′ end throughout the text. A substrate strand consisting of a single-stranded toehold domain (t*) and a branch migration domain (a*) is initially hybridized to an incumbent strand (OUT) to form duplex A. The input (or invader) strand IN is complementary to both the toehold (t) and branch migration domains (A) of the substrate strand. Displacement is initiated by binding of IN to the toehold (via t/t*) followed by a three-way branch migration process in which base pairs between the incumbent and substrate strands dissociate and are replaced by base pairs with invader IN. The reaction is complete once the incumbent strand (OUT) is fully displaced from duplex A.