Biomolecular Computing Devices in Synthetic Biology - Advancing Artificial Intelligence Through Biological Process Applications - page 252

computations in vivo , that is, able to process
information inside living systems.
In this chapter, we will look at several simple
examples that will give readers an overview of
this marriage. These examples will be biomo-
lecular devices based on biological principles
that process information. In fact, we will look
at NOT and AND logic gates built using genetic
circuits (Weiss, 2003); the logic AND built using
just nucleic acids that works thanks to competi-
tive hybridization and toeholds (Fontana, 2006;
Seelig, 2006), and a nanodevice composed of a
DNA hairpin that opens and closes through genetic
regulation. Finally, we will consider an automaton
that diagnoses disease by checking for the pres-
ence of different RNA molecules associated with
the disease in question and releases the drug if
the diagnosis is positive (Benenson, 2004). This
is a beautiful example of the marriage of biomo-
lecular computation and synthetic biology with
a promising application in biomedicine.
Other devices, noteworthy because they were
the first to merge biomolecular computing and
synthetic biology, are a genetic toggle switch
with two stable states (Gardner, 2000), and the
repressilator, which is an oscillatory gene net-
work composed of three repressors (Elowitz,
2000). Both of these devices were designed in
vivo . Another circuit with two stable states was
designed in vitro (Kim, 2006). Being extracel-
lular, this circuit achieves better control of the
circuit parameters.

biomolecular computation and systems biology.
Systems biology is also a relative new and emerg-
ing field that can help to move synthetic biology
and biomolecular computation forward.

Synthetic biology: is a discipline half-way
between science and engineering (Benner, 2005;
De Lorenzo, 2006; ETC group, 2007). It is con-
cerned with:

• The design, construction and modification

of biomolecular systems and organisms to
perform specific functions.

• To get a better understanding of biological

mechanisms.

The operation of these synthetic biomolecular
systems is based on the processes of the central
dogma of molecular biology, that is, DNA rep-
lication, and especially DNA transcription and
translation. But there are also designs that are
based on more specific biological processes like
the competitive hybridization of nucleic acids,
the operation of certain enzymes, etc.
There are at present two trends, bottom-up
and top-down, in synthetic biology projects
(Benner, 2005):

• The bottom-up trend takes the form of a

hierarchy inspired by computer engineering
(Andrianantoandro, 2006). The building
blocks are DNA, RNA, proteins, lipids,
amino acids and the other metabolites.
These building blocks interact with each
other through biochemical reactions to form
simple devices. The devices are linked to
form modules that can do more complex
tasks. These modules are connected to set
up biomolecular networks. These networks
can be integrated into a cell and change
the cell's behaviour. The DNA sequences
with special functions, like the operator,
the promoter, etc., are called BioBricks in
synthetic biology. And there are propos-

SyNTHETIC bIOLOGy,
bIOMOLECULAR COMPUTATION
AND SySTEMS bIOLOGy

The definition of synthetic biology is changing
and the borders of this discipline are fuzzy. In the
following, we will try to give a comprehensive
definition that includes the most relevant research
that is being developed and could be considered
to be part of this field. We will also describe