Figure 2.
Chemical operation of hybrid DNA/enzyme circuits. By a slight abuse of notation, Xi refers either to the output Xi or its specific domain. The number-labelled domains are global, shared by all outputs. The letter-labelled domains are specific to an input or output. (a) Strand displacement performs pseudo-weighted-sums of the inputs concentrations. An input Xi displaces an inhibitor Ii from a weight complex Wij = Ii : Tj to give an active template Tj. (b) Amplification. A template Tj catalyses the replication of Yj through a mechanism mediated by a polymerase and a nicking enzyme. Binding of the output Yj to the template triggers its elongation by the polymerase and nicking by a nicking enzyme. Spontaneous melting releases the outputs. (c) Degradation. Outputs are continuously degraded by an exonuclease enzyme which hydrolyses single-stranded DNA.