Figure 3: This diagram illustrates the “branch migration” DNA reaction, in which one complementary strand is paired with—
and replaces the existing partner of—another strand.
molecules modified with additional
Moreover, DNA can be used to actuate DNA structures. DNA tweezers developed by Yurke are one typical example, where the single strand called fuel
triggers the conformational change of
DNA tweezers by branch migration [ 9].
Along this line, various kinds of motors
and walkers made of DNA molecules
have been developed [ 5].
Imagining the use of computers is easy
in the context of construction of automobiles or other computers. However,
imagining the use of computers to
make robots made of cells or DNA is
much more difficult.
IT is used heavily in general biologi-
cal research. Methods for string search
and string comparison are commonly
used for searching for unknown chro-
mosome sequences and for comparing
gene sequences among species. Such
methods are becoming increasingly im-
portant due to the progress in sequenc-
ing technology, while gene sequencing
itself requires methods for assembling
fragments of gene sequences, which is
also a kind of string processing.
Figure 4: Starting with the AND gate and reading clockwise, we see the input and
output of each step in the process of computing a Boolean AND via the branch
are too detailed as models and not
appropriate for biological systems because the parameters in the differential equations are often unknown. In
addition, stochastic aspects are often
important inside a cell because the
copy number of a particular molecular
species is very small. The copy number
of each chromosome is only one. Consequently, more abstract discrete models are also used for modeling biological systems, and stochastic simulation
is used to analyze such models.
Unlike systems biology, synthetic
biology tries to construct artificial systems. Using genetic components found
in natural systems is not necessary for
this. We are free to engineer whatever
components are required for easy use.
The MIT researchers who initiated
the study of synthetic biology take a
rather radical approach to introducing
engineering disciplines into biology.
In particular, they emphasize standardization and abstraction [ 2]. More
specifically, they are compiling a registry of genetic components or parts,
similar to a transistor data book, and
are trying to standardize the registry
by adding various quantitative data
to the component descriptions. Such
standardized components can be used
without knowledge of their internal
However, because biological components extracted from natural systems
usually interact with one another in
an unexpected manner, identifying all
possible interactions among them is
not possible. Even if they are standardized or abstracted, some unexpected
interactions still remain, which makes
the straightforward composition of
components difficult. Moreover, biological components are usually fragile
and exhibit stochastic behaviors, which
can be regarded as errors from the artificial systems perspective. Therefore,