Biomolecular Computing Devices in Synthetic Biology - Advancing Artificial Intelligence Through Biological Process Applications - page 262

Figure 8. Hairpin operation

The hairpin switches from open to closed when
gene F' is activated and transcribes the fuel-strand
F' , which is completely complementary to F . Then,
F' recognizes and binds to the toehold of F . It then
displaces the 3' end and totally hybridizes to F
to free the hairpin. The 3' and 5' ends hybridize
and the hairpin closes. Note that each open and
close cycle yields a double-stranded waste product
F-F' . This device can operate as a biosensor that
measures the concentration of proteins activating
the F gene, for example. The concentration of the
open and closed hairpins indicates the result of
the measurements.
Nanodevices similar to the hairpin, like twee-
zers with two bonded fluorophores that indicate
whether the tweezers are open or closed, have
been designed and built (Yurke, 2000). When they
are closed the fluorescence intensity emitted by
the fluorophores is less than when they are open.
Additionally, tweezers open or closed states are
also controlled by genetic regulation (Dittmer,
2004; Dittmer, 2005). These new devices can
measure the concentration of proteins or other
biomolecules and work like biosensors.

EXAMPLE OF A bIOMOLECULAR
AUTOMATON

It is now possible to program biological computers,
namely, computers made mostly of DNA that work
like automata, i.e. like programmed nanomachines
(Benenson, 2001; Benenson, 2004; Stojanovic,
2003). A finite automaton is a computer with a
finite number of states that uses transition rules
to process a finite number of symbols and pass
from one state to the next.
Figure 9 is a biological computer that work
like an intelligent drug (Benenson, 2004). This
automata is programmed to measure the pres-
ence of three different types of RNA molecules
associated with a disease ( RNA 1, RNA 2 and
RNA 3), and, if all three are present, free an RNA
strand that acts like a drug. The computer works
like a finite automaton with two states: yes and
no . The automaton's state is represented by the
hairpin's exposed toehold in Figure 9. The pos-
sible exposed toeholds are: