Biomedical Engineering Reference
In-Depth Information
a
b
c
F1
S
1
A
S
B
S
2
F2
Fig. 6.6
Conformation changes in a nanomotor: (
a
) closed state, (
b
) opened state, and (
c
) substrate
cleaving for return in the closed state
Fig. 6.7
Analyte sensing
through conformation
changes: (
a
) integrated-ligand
sensor and (
b
) coupled-ligand
sensor. The direction of
current flow by the
arrow
a
AQ
detector
A
b
AQ
sensor
A
detector
The DNA nanomotor consists of the A strand terminated with two fluorophores,
FAM and TAMRA (denoted by F1 and F2 in Fig.
6.6
), and the B strand, which
contains an RNA-cleaving 10-23-DNA enzyme that binds to the DNA/RNA
chimera substrate S and cleaves it into the fragments S
1
and S
2
. When not in
contact with the substrate, the B strand is in collapsed state, and the nanomotor
takes its closed conformation. Because of the resonance energy transfer between
FAM and TAMRA, the green FAM signal at 520 nm has a low intensity in this
state, and the yellow TAMRA signal at 568 nm is high. When it binds to S, the
DNA enzyme takes a bulged duplex form pushing apart the rigid parts and adopting
the open state. Now, the FAM signal increases, and the TAMRA signal decreases.
Subsequently, the bounded enzyme cleaves the substrate in smaller parts with a
lower affinity for the enzyme, which can therefore dissociate from the nanomotor.
The DNA nanomotor returns thus to the closed state, ready for a new cycle, and its
autonomous operation lasting as long as the substrate, which acts as fuel, is not fully
consumed. On average, 20 substrate molecules are consumed each half hour. As the
motor cycled, the fluorescence signals decrease due to dye photobleaching.
Conformational changes of DNA strands can be exploited for sensing specific
analytes. Examples of such electrical sensors are described in
Fahlman and Sen
(
2002
) and illustrated in Fig.
6.7
. The sensing principle is based on the finding that
the electrical transport in DNA, which is a multistep hopping process, is hindered
by mismatches and bulges in double-strand molecules. In particular, a bulge can be
caused by aptamer sequences in dsDNA. In the presence of the adenosine analyte
(denoted by (a) in Fig.
6.7
), however, which binds strongly to the aptamer but not to
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