Molecular automatons could detect and treat disease in the body
29 June 2009
Researchers from the Artificial Intelligence Group (LIA) at the
Universidad Politécnica de Madrid's School of Computing have designed a
biomolecular automaton and several genetic circuits with potential
future applications in the field of vanguard medicine.
Depending on how it is programmed, the molecular automaton detects
DNA or RNA signals in vitro. In the future, though, provided it passes
all the experimental tests, it will be able to operate inside the human
The ultimate aim of a molecular automaton is to detect and treat
diseases in situ inside a human organism. Fitted inside the
organism, the automaton detects anomalies and dispenses the right
medicine at the right time. Biomolecular automata are artificial devices
built with biomolecules and designed to operate inside a living
These automata are engineered by first drafting a pencil-and-paper
design or specification. Then a mathematical model is built describing
the equations governing its operation. This is followed by a computer
simulation. Finally, the automaton is implemented in a biotechnology
laboratory. The whole process will be repeated cyclically until the
automaton has the desired features and functionality.
The design and application of programmable molecular automata to the
diagnosis and in vivo treatment of diseases (also known as intelligent
drug) is a recent and promising application of DNA computing to
biomedicine, which was initiated by Prof. Yaakov Benenson in 2004.
The new biomolecular automaton designed and modelled at the UPM's
School of Computing has been sent to the Technische Universität
München's nanobiotechology laboratory for implementation and, if it
works, will be applied to medical research.
The LIA has also designed several circuits or synthetic biological
oscillators, whose job is to synchronize the activity of biomolecular
automata in a living system.
One of the synthetic biomolecular circuit designs developed by this
group was presented at the 3rd International Workshop on Practical
Applications of Computational Biology & Bioinformatics (IWPACBB'09) to
be held in Salamanca (Spain) in mid June.
The synthetic genetic circuit to be presented at Salamanca outputs a
biological signal. The signal concentration alternates at regular time
intervals and can be used as a clock signal for synchronizing biological
processes. The clock signal frequency of this oscillating circuit can be
modified (faster or slower clock), and it will act on a biological
circuit in the same way as the clock signal in digital computers.
This design will also be implemented at the Technische Universität
München and, if it works properly, will be donated to the Registry of
Standard Biological Parts, the open source genetic circuits design
database maintained by the Biobricks Foundation, associated with MIT.
This circuit or genetic oscillator is to be used as a module for
synchronizing the activity of other modules of a more complex genetic
circuit or as a synchronization signal controlling the activity and the
operating rate of a set of biomolecular automata. These oscillating
circuits are like traffic lights deployed inside a cell or a bacteria
that control and regulate the operation of the other circuits or
The aim of this project, which started in 2006 and is to finish at
the end of 2009, is to advance natural computing and systems biology
using a cell-inspired distributed computing model (called P system or
membrane computing), as well as to develop synthetic biology by
designing new circuits and biomolecular automata.
As a branch of science, natural computing has two goals: understand
the computational processes taking place in nature (particularly,
biology) and develop computational models inspired by nature.
Systems biology pursues the challenge of developing robust and
precise mathematical models whose application can describe, understand
and make predictions on complex biological systems and processes. The
budding discipline of synthetic biology aims to design and build new
devices and artificial biological organisms, as well as redesign and
reprogram natural biological systems.
This project, led by School of Computer professor Alfonso
Rodríguez-Patón and researched by doctoral candidate Jesús Miró Bueno,
has been funded by the Spanish Ministry of Education and Science
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