Biomolecular Machines - Bionanoelectronics: Bioinquiring and Bioinspired Devices - page 182

Complementary strands to the input ssDNA remove the header from the footer
because the input strands hybridize with their complementary DNA sequences. A
new cycle of events can start.
Another DNA-based walker that can move forward or backward on a ssDNA
track depending on the sequence of the ssDNA fuel is described in Bath et al.
( 2009 ). As for a kinesin motor, its movement is based on the coordination between
two identical single-stranded DNA feet attached to the 3 0 end of a double-stranded
spacer. The track consists of a sequence of ten nucleotide-binding domains and
six nucleotide competition regions, the feet competing for hybridization to the
competition domain. When the 5 0 end of one foot is lifted from the track as a
result of this competition, it can bind to the fuel, which initiates the next step by
a series of strand displacement, strand cutting by a nicking enzyme, dissociation,
and rehybridization to the track processes. The directional bias of the walker relies
on a ratchet mechanism determined by the preferential interaction of the fuel strand
with one of the two feet.
An example of a unidirectional DNA walker that moves along a DNA track
can be found in Yin et al. ( 2004 ), and the processes involved in a single step (two
consecutive steps are detailed in Yin et al. ( 2004 )) are illustrated schematically in
Fig. 6.10 . The track contains anchorage sites denoted by A and B on which the
six-nucleotide walker, indicated by , can bind. Initially, the walker is positioned
at A, forming the A complex. Then, anchorages A and B ligate, because
they have complementary sticky ends, form the A B molecule in an irreversible
energy-consuming process and create a recognition site for a cutting enzyme,
which cleaves the structure and transfers the walker to the anchorage site B.
The newly formed complex, B , can be transferred to another anchorage site
if the sequence of processes described above are enabled; the cutting enzymes
(endonucleases) involved in subsequent steps can be different. Backward movement
is not possible since the previous restriction site is destroyed by the cut and
a new site is created at each ligation. The energy source is the hydrolysis of
adenosine triphosphate, and the motion of the walker can be monitored by gel
electrophoresis.
DNA displacements on a DNA track can also be driven by polymerase 29,
which is an enzyme that replicates DNA or RNA templates ( Sahu et al. 2008 ). DNA
displacement from its template or cargo transport occurs in this case by extension of
a primer hybridized to the template. Transportation by polymerase-driven processes
takes place at a relatively high speed of 680 nm min 1 .

a b c

A*

B*

A

B

A*B

Fig. 6.10 Unidirectional DNA walker: ( a )thewalker is positioned at A, ( b )theA B molecule
is cut by an enzyme, and ( c ) the walker is positioned at B