Biomedical Engineering Reference
In-Depth Information
Fig. 6.2
pH-driven
conformation change of a
DNA molecule between a
quadruples state (
a
)anda
rigid state (
b
)
a
b
F
+
F
gold
gold
a
b
c
CF
B
F
D1
A
+
+
+
C
D2
Fig. 6.3
Conformation changes of a DNA tweezer from the opened state (
a
) into the closed state
(
b
) and back again (
c
)
cytosine stretches. The CH
C
complexes are absent in basic pH solutions when, in the
presence of complementary strands, DNA hybridizes into a straight, linear structure.
To monitor the nanomotor, a rhodamine green fluorophore F is attached at the
3
0
end of the DNA strand, which is immobilized via gold/thiol self-assembly on
precise locations on a microstructured gold layer deposited on a glass substrate. In
the quadruplex state, F is quenched by the nearby gold surface due to the efficient
energy transfer mechanism, while in the hybridized state, F is lifted up with about
2.5 nm and emits a green fluorescent signal four times stronger than in the closed
state. The nanomachine is highly reversible upon cyclic pH changes that transition
from one state to another, taking place in less than 5 min. If the DNA molecules are
immobilized on the surface of a cantilever, it is possible to measure the force exerted
during the conformation change. It was found that the open-to-close stroke of a
single motor induced a force of about 11 pN m
1
, which corresponds to 32 mN m
1
compressive stress on the surface of a silicon cantilever with length, width, and
thickness of 500m; 100m, and 1m, respectively (
Shu et al. 2005
). Oscillations
of the pH value can be produced by a nonequilibrium chemical reaction involving
oxidation of sulfite, which generates protons, and oxidation of thiosulfate, which
consumes protons, in a solution of sodium iodate (
Liedl and Simmel 2005
). The
pH-driven conformational switch between quadruplex and straight DNA molecules
is more stable, in the sense that the closed and open states become strongly locked,
if C
60
fullerenes are attached to both 5
0
and 3
0
ends of DNA (
Shin et al. 2009
).
The closed state is also more compact in this case, and the force and power stroke
generated by the nanomachine increase.
Among the first molecular machines ever fabricated is that in
Yu r k e e t a l .
(
2000
).
In this conformational switch, DNA is both fuel and machine material. As shown
in Fig.
6.3
, the switch commutes between opened and closed states if ssDNA fuel
strand F and its complementary CF are introduced, respectively, the waste duplex
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