Figure 9.

Cross-catalytic DNA hairpin system [55]. (a) The input complexes A, B, C, D, I, and output complexes AB, CD. Species A has a fluorophore/quencher pair attached (shown as star and dot in the figure), which is initially separated by about 6 nt (quenched), and presumably much further apart (not quenched) after the initiator starts invading at the helix end. (b) Peppercorn enumerates nine condensed reactions: three reversible and three irreversible. The initiator I starts a catalytic process where A and B are consumed to form AB; AB itself is a catalyst to produce CD, and CD is a catalyst to produce AB. The three ‘reverse’ reactions in this system are unimolecular remote-toehold interactions. (c) Simulations of the enumerated system at different concentrations of the initiator I. The trajectories start at [A]₀ = [B]₀ = [C]₀ = [D]₀ = 20 nM and show the decrease of species A over time. The dashed black line marks the 50%-completion time, which was used to compare with experimental data in figure 11. Colour scheme corresponds to fig. 3 in Yin et al. [55], which shows experimental data. Runtime for enumeration (T_E) and condensation (T_C) on a PC (i5-4300U CPU @ 1.90GHz): (c) T_E + T_C = 274 ms.