Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 236

Fig. 11.11 Deoxyribozyme-based molecular walker and origami prescriptive landscape

(Reprinted by permission from Macmillan Publishers Ltd: Ref. [ 69 ], copyright 2010)

an improved system, achieving the coordination of the two feet and processivity
[ 66 ]. This system consists of a rigid footpath and a bipedal walker with two different
single-stranded feet (A and B). The 49 nm double-crossover (DX) footpath is
decorated in a directionally polar manner with different metastable DNA hairpin
motifs (each consisting of one “signaling” and one “foothold” strand). The walker
comprises two different single-stranded feet that are chemically linked via a covalent
5 0 -5 0 bond. Overall, processivity is guaranteed by signaling strands that mediate the
interaction between feet and fuel strands in a way that only one foot could detach
from the track. Directionality is achieved through the hybridization of metastable
hairpin fuel strands to the footpath (a “burnt-bridges” mechanism). Seeman and
coworkers demonstrated a full walking cycle of their device by covalently cross-
linking a radioactively labeled walker (32P) to its track in successive walking
states and observing fragments with characteristic mobilities during autoradiogram
analysis of denaturing PAGE. Another construction, in which the footpath can be
reused, was reported by Turberfield and coworkers [ 67 ](Fig. 11.10 c). The walker
has two feet that can hybridize to a single-stranded footpath with overlapped binding
sites. The two identical feet bind competitively to the overlapped sites that cause the
leading and trailing foot to interact with the fuel at different rates, which is capable
of directional and processive motions.
In order to bring the one-dimensional track walkers forward to make more
complex movements, Lund et al. recently integrated DNA origami technology with
the previously reported molecular spider structure [ 68 ] to make a step closer to
creating molecular robots [ 69 ](Fig. 11.11 ). The molecular spider in this approach
comprises one streptavidin molecule as an inert body and three catalytic legs
which are adapted from the 8-17 DNAzymes. This DNAzyme binds and cleaves
oligonucleotide substrates with a single ribose moiety into two shorter products that
have lower affinities for the DNAzyme. An array of the oligonucleotide substrates
are immobilized to the surface of the DNA origami to form a walk track which