Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 233

Fig. 11.9 ( a ) Cartoon depiction of biped system taking a full step (Reprinted with permission
from Ref. [ 57 ]. Copyright 2004 American Chemical Society). ( b )Designofwalkerlocomo-
tion (Reprinted with permission from Ref. [ 58 ]. Copyright 2004 American Chemical Society).
( c ) Scheme of a walking DNAzyme and its track (Reproduced from Ref. [ 62 ] by permission of
John Wiley & Sons Ltd)

11.3.2.3 DNA Walkers

The first-generation DNA walkers share the same concept of generating the walk
motions. Sherman and Seeman reported the first DNA walker consisting of two
“feet” that were connected with flexible single-stranded linkers [ 57 ](Fig. 11.9 a).
Each foot is a DNA duplex with a single-stranded extension that is capable of pairing
with the complementary strand, called “foothold,” equipped on a triple-crossover
(TX) molecule, which is referred to as “footpath.” The two feet of the bipedal walker
are initially attached to the adjacent footpaths by two set strands, each of which has
an eight-base toehold allowing the set strand to be removed by the unset strand.
In the presence of the unset strand that specifically releases the leading foot from
the foothold, the leading foot is lifted and connected to the footpath only through
the flexible linkers. As for the leading foot taking a step forward, the set strand
complementary to the leading foot and the next foothold is added into the solution.
Consequently, the leading foot moves a 2 nm step along the footpath, leaving an
unoccupied foothold in the middle of the two feet. The flexible linkers that are long
enough to extend across two footholds ensure the motion. Then similar unset and
set operations are used to move the trailing foot ahead. Now the bipedal walker
accomplishes an inchworm-like movement and is ready for taking a next step. The
movement of the walker was demonstrated and monitored by gel electrophoresis.
Inspired by kinesin movement along a microtubule, Shin and Pierce constructed a
bipedal DNA walker adopting the similar principle to Seeman's design but driving
the motion by advancing the trailing foot to the lead at each step [ 58 ](Fig. 11.9 b).
Tian and Mao generated a system involving a different kind of unidirectional motion
which they called “molecular gears” [ 59 ]. This system contains two gears, each
of which is a DNA duplex circle composed of one central circular strand (C) and