Biomolecular Computing Devices in Synthetic Biology - Advancing Artificial Intelligence Through Biological Process Applications - page 258

tion is equivalent to a logical '0'. The logic gate is
composed of the gene (with its promoter, operator
and terminator), the concentration of repressor
proteins and the other biomolecules required for
translation and transcription (like, for example,
the ribosomes that synthesize the repressor protein
from the input-RNA or the RNA polymerase that
synthesizes the output-RNA).
In the following we explain how this NOT gate
works. Figure 2-a illustrates the case of the input
'1' and output '0'. The input '1' is equivalent to a
high concentration of input-RNA that results in a
high concentration of gene repressor protein that
stops the RNA polymerase from progressing. Con-
sequently, the gene is inhibited for a longer time
and produces a low concentration of output-RNA,
or, in other words, we get '0' at the output.
Note that concentrations are said to be low not
zero because repressor proteins generally never
manage to inhibit the gene completely and a
minimum concentration of RNA is always formed.
This is termed the basal concentration.
Figure 2-b illustrates the case of the input '0'
and output '1'. The input '1' is equivalent to a low
concentration of input-RNA that results in a low
concentration of repressor protein. Consequently,
the gene is activated for a longer time and produces
a high concentration of output-RNA, or, in other
words, we get '1' at the output.

NOT gate, a high concentration of biomolecules
matches a logical '1' and a low concentration a
logical '0'. The logic gate is composed of a gene
(with its promoter, operator and terminator) and
the biomolecules required for transcription (unlike
in Figure 2, Figure 3 illustrates RNAp).
In the following we explain how this AND gate
works. The protein is at first inactive. It needs to
bind to the inducer to be activated and be able to
bind to the operator. When the concentrations of
the inducer and the inactive protein are high, i.e.
when there is a logical '1' at both inputs, the ac-
tive protein concentration is high. Then the gene
is activated for a longer time. This promotes the
binding of the RNAp to the promoter and yields
a high concentration of mRNA, i.e. we have a
logical '1' at the output.
On the other hand, when the concentration
of the inactive protein, the concentration of the
inducer or both concentrations are low, i.e. when

Figure 2. NOT gate

Genetic Circuit Operating as a Logic
AND Gate

An AND gate can have more than one input and
an output. If all inputs are '1', the output will be
'0'. In all other cases the output is '0'. Figure 3
is an example of an AND gate with two inputs
made of biomolecules (Hasty, 2002; Weiss, 2003).
It represents the case where the two inputs are
'1'. One of the inputs is the concentration of an
inducer molecule (Input 1). The other is the con-
centration of an activator protein (Input 2). The
output is the concentration of mRNA resulting
from the gene transcription. As in the case of the