Extended Data Fig. 6: Experimental optimization and performance evaluation of WIR2 and WIR3.
From: DNA-based programmable gate arrays for general-purpose DNA computing
a, Molecular reactions for wiring (for WIR2) or reading out (for WIR3) an output signal from a gate. Low (green) and high (red) signals are transmitted independently. The dashed lines indicate the upstream binding region. b, To introduce the threshold-over-amplifier binding priority, the duplex region was shortened by 2 bp, which minimized non-specific input-threshold binding and the leakage. c, Without Threshold, output from a gate could be amplified to close to 1. However, weak signal leakage could also be amplified, leading to false result. Thus, the threshold is essential to suppress leakage before amplification. d, We used a Threshold molecule (Th) that could interact with output quickly. With 0.4× leakage signal, we found Th with a concentration higher than 0.4× can effectively suppress leakage. With 1× output signal, we found signal transmission speed decreased with Th concentration. To balance leakage suppression and computing speed, we used 0.4× to 0.6× Threshold for experiments. e, Signal wiring for High signal (left) and Low signal (right) using 0.4× threshold.
