Figure 6.

(a) Ratio of the catalyzed to leakage reaction rates (k_cat/k_leak) for single location fuel modifications to evaluate overall system performance. Catalyzed reactions were performed with the catalyst (1 nM), fuel (13 nM), substrate (14 nM), and reporter (20 nM), monitored via fluorescence, and uncatalyzed leakage reactions were performed with fuel (1300 nM), substrate (14 nM), and reporter (20 nM). The black bar represents the original fuel strand. Pink, orange, and blue bars represent 1 and 2 nt modifications at 5′, nick, and 3′ locations, respectively. Error bars show the standard deviation from the mean for select samples in triplicate to estimate experimental error. (b) Representative fluorescence data of catalytic reactions: the original fuel (empty black circles), G₁T₂ modified fuel (empty red triangles), C₂₄T₂₅ modified fuel (yellow diamonds), and G₄₃A₄₄ modified fuel (empty blue stars). (c) Representative fluorescence data of leakage reactions: the original fuel (solid black circles), G₁T₂ modified fuel (solid red triangles), C₂₄T₂₅ modified fuel (solid yellow diamonds), and G₄₃A₄₄ modified fuel (solid blue stars). The gray lines are the calculated fits to each curve, and the solid blue and purple lines represent reactions between the reporter and the original fuel and the reporter and the substrate, respectively.