Biomolecular Machines - Bionanoelectronics: Bioinquiring and Bioinspired Devices - page 186

Fig. 6.14 Undercut
geometry of microchannel for
efficient microtubule guiding

channel

undercut

Fig. 6.15 Biomolecular

sorter

CYTOP

cover

sorter region

geometrical constraints for diffusing into the channel are the least restrictive. The
guiding efficiency of microtubules along kinesin-coated channels increases for a
channel geometry that includes an undercut, which prevents microtubules to climb
the sidewalls (see Fig. 6.14 )( Hess et al. 2003 ). The height and depth of such an
undercut are 200 nm and 1m, respectively.
An autonomous highly selective biomolecular sorter based on kinesin/microtubule
interactions has been shown in Lin et al. ( 2008 ). The device, represented
schematically in Fig. 6.15 , consists of functionalized microtubules that move
along kinesin-coated petal-shaped microchannels etched in the CYTOP polymer
film. CYTOP surfaces inhibit the displacement of kinesin-driven microtubules,
providing selective confining of the microtubules in the channels. The microtubules
bind to a specific cargo protein from a dilute solution and are guided by the sorting
channels to a collector region in the center of the structure, in which they become
trapped. The channel petal shape avoids microtubule loss at sharp corners, while
arrow-shaped patterns in the collector region prevent microtubule escape from
the trap. The collector region is protected by a parylene cover, which increases the
trapping efficiency. Experiments with microtubules labeled with the fluorescent dye
TMR showed that the intensity of the fluorescent signal increases rapidly and then
saturates after 45 min, the density of trapped microtubules in the collector being
100 times higher than in other parts of the device. Analyte sorting can be achieved
by binding microtubules to specific molecules.
DNA machines are not only passive, in the sense that they process, detect,
or transport other molecules, but can be also active, multiplying the amount of
molecules in a solution. For instance, an autonomous isothermic DNA machine can
amplify the detection of M13 phage ssDNA sequences ( Weizmann et al. 2006 ).
In this case, the machine is activated upon recognition of the viral DNA that must
be analyzed and synthesizes a DNAzyme, which allows visual monitoring of the
reaction by chemiluminescent or colorimetric imaging. The peroxidase-mimicking
enzyme is synthesized on a DNA template. The sensitivity level of virus detection
is 10 14 M.