Biomedical Engineering Reference
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the dsDNA, the bulge distortion lessens due to internal stacking and folding of the
aptamer loop and allows electron flow to occur along the duplex structure, between
the anthraquinone oxidant AQ, tethered at one end of the molecule, and the detector
stem. The configuration in Fig.
6.7
a is called integrated-ligand sensor, while that
in Fig.
6.7
b is the coupled-ligand sensor. The properties of the latter sensor are
independent of the conductivity of the folded aptamer domain.
6.2
Biological Walkers
This section focuses on biological machines able to change their position along a
track, which is typically a DNA molecule, mostly by conformation changes. A DNA
biped walker that can move along a track in both, forward and backward, direction
has been demonstrated in
Sherman and Seeman
(
2004
). A schematic description of
its stepped movement is illustrated in Fig.
6.8
, where W denotes the biped walker,
T is the track, consisting of a triple-crossover molecule with footholds FH, and P
are psoralen molecules, which cross-link DNA strands covalently if irradiated. In
Fig.
6.8
, the double-stranded parts of W and T are represented by thicker regions.
The walker contains two double-helical rigid parts connected by flexible strands
of ssDNA, consisting of nine nucleotides, each rigid part terminating with a ssDNA
foot. The foot can attach to a foothold in the presence of strands S
i
;i
D
1,2,3,that
are complementary to both of them and have an additional 8-base toehold, which
allows removal of the strand by a complementary strand CS
i
in the solution. If
one of the feet is released from the corresponding foothold due to the presence
of CS
i
, which completely hybridize to the strand S
i
following branch migration,
it can extend to the adjacent foothold to which it becomes attached with the help
a
b
W
+
+
CS
2
S
3
P
S
1
S
2
FH
T
c
+
Fig. 6.8
DNA biped walker:
(
a
) the two feet are attached
to the track, (
b
) the leading
foot moves to the next
position, and (
c
) the trailing
foot follows
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