AAWSAP DIRD, Quantum Computing and Utilizing Organic Molecules in Automation Technology, December 2010

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Combining DNA enzymes with stem-loop controllers yields a variety of fundamental
logic gates that use short strands of DNA as both inputs and outputs. The cleaving
action of the enzyme produces the strands that serve as the gate's output of 1. No
cleaving is an output of 0.
AND GATE
A logical AND gate has two inputs and produces an output of 1 only if both inputs are 1.A deoxy-
ribozyme with a stem-loop on each of its arms acts as an AND gate. The closed stems disable the
enzyme (left), and only when both loops' matching input strands are added can the enzyme
cleave substrates (middle). Truth table (right) summarizes the gate's function.
0
0
0
E
AND-AND-NOT GATE
A stem-loop controller on the "back" of a deoxyribozyme acts as a NOT
input that inhibits the enzyme when the matching input strand is pres-
ent. If the stem-loop's input strand is not present (0), the stem remains
0
0
closed and the enzyme cleaves substrates to produce output strands,
provided that the enzyme's arms are free (left). When the input strand
binds to the controller, the stem opens, deforming the enzyme core and
rendering it inactive (middle). A deoxyribozyme with controllers on
0
both arms and its back thus behaves as an AND-AND-NOT gate. The
enzyme is active, cleaving substrates and thus producing the 1 output,
only if inputs X (blue) AND Y (purple) AND NOT Z (yellow) are present.
0
E
0
0
0
0
Figure 21. Simplistic rendering of a DNA logic gate.
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