Extended Data Fig. 6: Three-species winner-take-all behaviour and rate measurements for selecting DNA sequences in winner-take-all reaction pathways.
From: Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks
a, Fluorescence kinetics data for a three-species winner-take-all circuit. Initial concentrations of the three weighted-sum species are shown on top of each plot as a number relative to a standard concentration of 50 nM (1×). The initial concentrations of the annihilator, restoration gates, fuels and reporters are 75 nM (1.5×), 50 nM (1×), 100 nM (2×) and 100 nM (2×), respectively. b, Measuring the rates of 15 catalytic gates. Fluorescence kinetics data (dotted lines) and simulations (solid lines) of the signal restoration reaction are shown, with a trimolecular rate constant (k) fitted using a Markov chain Monte Carlo package (https://github.com/joshburkart/mathematica-mcmc). The reporting reaction was needed for the fluorescence readout. Initial concentrations of all species are listed as a number relative to a standard concentration of 50 nM. c, The 15 catalytic gates sorted and grouped on the basis of their rate constants. All rate constants are within ±65% of the median. The two coloured groups of three rate constants are within ±5% of the median. These two groups of catalytic gates were selected for signal restoration in the winner-take-all DNA neural networks that remember two to nine 100-bit patterns (Methods section ‘Sequence design’).
