Biology Reference
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become a key focus of foundational synthetic biology. Examples include the ra-
tional design of RNA-based mRNA translation regulation and metabolic sensing
[10], [11], modular systems for controlling mRNA stability [12], and a design-
able way of implementing RNAi-based combinations circuits in mammalian cells
[13]. While there are still subtleties and a variety of case-by-case issues, these all
exploit the relatively simple structural rules in RNA, Watson-Crick complimen-
tarity rules, and the relative ease of RNA in vitro evolution to design families
of parts with more or less predictable function. There has also been progress in
engineering protein-based parts families. It is becoming ever more possible to, for
example, design zinc finger proteins as transcription factors [14] or to gain control
of eukaryotic scaffolding proteins to design signaling switches [15] and more.
Even with the increasing sophistication of synthetic biological parts families,
challenges remain in the scalable design of complex regulatory circuitry. Because
of the lack of spatial addressing of “signals” between components, like wires be-
tween physically separated components in an electronic circuit, it is generally not
possible to reuse the same biological component in the same way as one could re-
use a transistor (exceptions include such things as ribosome binding sites to some
degree [16]). This leads to heterogeneity of “device physics” across the circuit,
as every part is somewhat different than every other and a necessity to actually
have a chemically different part for every elementary operation of the circuit. The
properties of these parts are often very complex, thereby making abstraction into
useful mathematics for design, such as Boolean logics, difficult. Further, imple-
menting all these different parts in a cell, were they available, might require fairly
large outlays of DNA real estate and place large energetic loads on the cell. Finally,
in most current synthetic biological applications, the “states” of the regulatory
circuitry are encoded in transient chemical concentrations that require energy
outlay to hold and can't be maintained after cell death or transmitted easily from
one cell to another.
For all these reasons above, circuits that might operate by changing DNA
sequence using, for example, recombinases are attractive complements to gene
expression and protein interaction networks. Operations on DNA tend to change
state (sequence) in a discrete, almost Boolean, fashion. The state may be main-
tained without constant energetic input, persists after cell death and even if rare in
a cell population a particular sequence may be amplified out from the background
by PCR. Further, since the “state” is encoded in DNA, it is possible by the various
mechanisms of inter-cell DNA transfer, such as conjugation to pass state-output
among cells as a complex form of communication as one iGEM team recently
suggested [17]. More subtly, as shown below, the ability to decide the spatial ar-
rangement of recombination sites provides the ability to create circuits with large
sequential state spaces accessible from relatively few recombinase inputs with ef-
ficient use of DNA.
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