Biomedical Engineering Reference
In-Depth Information
strands on the arms of tweezer B, closing it. Furthermore, the activation of the two
states I and II by the two inputs, AMP and adenosine deaminase, represents a SET-
RESET logic operation, concluded from the truth table. However, the introduction
of the enzyme is also followed by a significant imperfection, the thermal activation
inducing the subsequent separation of the DNA construct, which was re-formed
upon cooling the system. The stabilization of the tweezers structure is prerequisite
for continuous operation of tweezers system. The two-tweezer system was improved
by Willner's group, by adopting the strategy of operating the tweezers in isothermal
conditions [
49
]. Briefly, the sequence, which folds up to i-motif conformation at
acidic condition, is introduced onto the arms of one of the tweezers. The i-motif-
encoded tweezers compete with another tweezers in capturing the target DNA strand
energetically, thus leading to the coherent activation of two tweezers by cycling the
pH between acidic and neutral value, at room temperature.
In the following research, the two-tweezers system was upgraded to a more
complex mechanical system by Willner's group, including three tweezers
'
,
“
,and
, instructed by six fuels (or called logic inputs, i.e., pH-acidic or basic, Hg
2C
ions
or cysteine ligand complexing Hg
2C
ions, and two complementary single-stranded
nucleic acids) [
50
]. The fuels are pairwise, in other words, consisting of three pairs,
each of which act reversely for the tweezers. The three-tweezer system is designed
in such way that pairing Hg
2C
ions/cysteine fuels the opening and closing of tweezer
'
”
, while the fuel strands open and close
all the three tweezers. In addition, the configurations of tweezer
, pH controls the configurations of tweezer
“
”
are also dependent
on tweezers
. When the fuels are alternatively applied to the three-tweezers
system, the mechanical motions of tweezers are activated cooperatively (Fig.
11.6
b).
Each tweezer is labeled with respective fluorophore/quencher pair at the ends of the
arms, recording the configurations of the tweezers as well as the outputs of the
system. As a result, a finite state automaton system, with 16 states (configurations),
8 outputs, and 6 inputs, is constructed on the basis of the operation of three tweezers
(Fig.
11.6
c). The system exhibited a memory because each current state and output
depended not only on the source configuration but also on past states and inputs.
Through integration of the concept of DNA machine with the logic computation
using new chemical stimulus and appropriate sequence design, Willner's group
implemented the first enzyme-free all-DNA automaton.
In a more recent research, Firrao and coworkers advanced the “tweezers” concept
to control the motion of a 2D DNA origami structure [
51
](Fig.
11.7
). They
fabricated a 2D DNA circular origami of an estimated total diameter of about
100 nm, consisting of an internal disk of an estimated total diameter of about 60 nm
and an external ring, of about 20 nm. In order to ensure the flexibility of the two
semihalves of the internal disk (named “wings”) so that they can bend relative to the
plane of the ring, four nucleotide spacers along the bending axis of the wings are
left uncomplementary as shown in green lines in Fig.
11.7
. Moreover, a 120-nt-long
single-stranded oligomer, the “probe,” is settled across the internal disk binding to
the sticky ends on the edges of the two opposite movable wings. In the presence of
the a “target” hairpin structure, in which the loop is perfectly complementary to the
central part of the “probe,” the formation of double strand causes a tensile force on
'
and
“
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