Fig. 1: Strand displacement and catalysis in DNA nanotechnology.
a Toehold-mediated strand displacement. The reactant duplex BD can be attacked by an invading strand A that is complementary to the whole of D, including an initially single-stranded toehold. b A simple catalytic motif engineered through toehold exchange. Displacement of B by A (which are complementary to different but overlapping domains of D) exposes a second toehold that allows the subsequent displacement of A by C. A can thus act as a catalyst for the interconversion of BD and CD, providing control over the reaction. c Addition of a fluorescent reporter for single-stranded B allows the progress of the reaction to be monitored. d Normalised fluorescence data showing the effect of adding catalyst A on the catalytic scheme in b with 22 bp duplexes and 6 nt toeholds. A total of 40 nM of BD is mixed with 200 nM of C and 250 nM of reporter complex, both with and without triggering by addition of 5 nM of A. Output in the absence of A (the leak reaction) is low, but the reaction yield after 500 minutes is limited, a problem exacerbated by the similar stabilities of reactant and product. A longer strand C2 that can form two extra base pairs with D (in the toehold domain for binding of A) increases yield over 500 minutes but at the cost of a loss of catalytic control: the leak reaction in the absence of the catalyst is now extremely strong. Each curve represents a single experiment; a repeat is shown in Supplementary Fig. 7. A full list of sequences is provided in Supplementary Table 6.
