Biomolecular Computing Devices in Synthetic Biology - Advancing Artificial Intelligence Through Biological Process Applications - page 257

prevent the RNAp from binding to the
promoter or block its progress, inhibiting
translation in both cases (inhibited gene).
On the other hand, the activator proteins
help the RNAp to bind to the promoter and
promote translation (activated gene). One
important property of the regulatory proteins
is that they can be activated or deactivated
by means of small molecules called inducers.
Note that a regulatory sequence is another
gene with its respective promoter, operator,
terminator and regulatory sequences. These
latter regulatory sequences are again other
genes with their promoters, operators, etc.
And all this makes up a complicated genetic
network.

EXAMPLES OF DIGITAL GENETIC
CIRCUITS

Genetic circuits are the most common devices in
synthetic biology. The operation of these circuits
is based on genetic transcription regulation. Most
of these devices are digital circuits, where the
logical '1s' and '0s' are equivalent to high and
low biomolecule concentrations.
One problem with genetic circuits is the as-
sembly of circuits with each other. The reason is
that, unlike electronic circuits where the input
and output signal is always voltage, the molecule
type representing the output signal of one circuit
might not be the same as the molecule type rep-
resenting the input signal of the next circuit, and
the two cannot be connected. The MIT has put
forward an idea to solve this problem. This idea
is to get a 'universal' measurement unit, called
PoPS (polymerase per second). PoPS represents
the number of mRNA molecules of a gene tran-
scripted per second.
Another problem is isolating the genetic circuit
when it is introduced into a cell to prevent parts
of the circuit interacting with parts of the cell or
prevent the biomolecules belonging to the circuit
propagating in the cell.
Two simple examples of digital genetic circuits
that perform the function of NOT and AND gates
are given below.

• Operon: in bacteria, the promoter, operator,

gene and terminator complex is termed op-
eron. A standard example is the Escherichia
coli bacterium's lac operon that codifies the
proteins required for lactose transportation
and metabolism. In this example, lactose
actually works as an inducer molecule.

• Transcription: process in which the RNA

polymerase enzyme copies a DNA strand
to a complementary RNA strand. The dif-
ferent types of RNA are messenger RNA
(mRNA), transfer RNA (tRNA), ribosomal
RNA (rRNA), small RNA (sRNA) and ri-
bozymes.

• Translation: process in which a ribosome

picks up amino acids to form a protein fol-
lowing the nucleotide sequence of a mes-
senger RNA strand.

Genetic Circuit Operating as a Logic
NOT Gate

A NOT gate has an input and an output. If the
input is '1', the output will be '0'. On the other
hand, if the input is '0', the output is '1'. In other
words, it works like an inverter. Figure 2 is an
example of a NOT gate made of biomolecules
(Weiss, 2002). The input is a concentration of RNA
molecules labelled as input-RNA. The output is a
concentration of RNA molecules labelled as out-
put-RNA. A high concentration of RNA molecules
is equivalent to a logical '1' and a low concentra-

• Replication: process in which the DNA

polymerase enzyme makes a copy of a
double strand of DNA.

Restriction or cutting enzymes: are proteins
that recognize certain subsequences of a DNA
double strand and cut the double strand at a par-
ticular site. The recognition and cutting sites are
enzyme specific.