Biomolecular Machines - Bionanoelectronics: Bioinquiring and Bioinspired Devices - page 181

Fig. 6.9 DNA biped walker:
( a ) one foot is attached to the
track, ( b ) the leading foot
moves to the next position,
and ( c ) the trailing foot
becomes the new leading foot

a b

W

S 2

+

CS 1

+

S 1

T

c

+

of strand S j . This first step of the biped walker is completed if the remaining
foot performs the same sequence of operations. The direction of movement is
controlled by the complementary input strands introduced in the solution. In this
walker configuration, one foot always trails the other.
A DNA walker that moves similar to the kinesin motor along a microtubule, i.e.,
by advancing the trailing foot to the lead, is described in Shin and Pierce ( 2004 )
and represented schematically in Fig. 6.9 . The walker W, which consists of partially
complementary ssDNA strands composed of a 20-bp helix section that joins two 23-
bp legs, moves along a DNA track T containing protruding 20-bp ssDNA branches
(three such branches are shown in Fig. 6.9 ) separated by scaffold helices with
a length of 15 bp. An input strand S1 forms a 18-bp helix with one leg of the
walker and another 17-bp helix with one protruding branch, anchoring the walker
to the track. In the presence of another strand S2, the other leg of the walker is
anchored to the neighboring protruding branch, while the addition of the CS1 strand,
complementary to S1, releases the initially bound/leading leg of the walker and
forms the waste S1-CS1 double strand; the initial leading leg becomes a trailing
leg. CS1 initially binds to S1 at a 10-bp overhang, a following strand displacement
process completing the generation of the waste product. The walker locomotion,
which proceeds in 5-nm steps, can be monitored by end-labeling the protruding
branches with different dyes and the walker legs with quenchers.
An addressable molecular tweezer somewhat similar to the walker in Shin and
Pierce ( 2004 ) contains a set of immobilized footer tweezers that self-assembly on
a DNA track and a free header tweezer that floats in solution such that it can close
any footer tweezer in the presence of a specific pair of fuel input ssDNA strand
( Chhabra et al. 2006 ). All tweezers are branched DNA junctions with four rigid arms
forming an X-shaped structure with an acute angle that has an average value of 60 ı .
Two arms which enclose the acute angle are terminated with single-stranded sticky
ends. In addition, the arms of footer tweezers with sticky ends contain also coupling
reactants. Then, when the sticky ends of the header and footer tweezers hybridize
with parts of the input strands, the footer tweezer is pinched. As a result, the two
reactants are brought close enough to trigger a coupling reaction that leads to an
amine bond, which covalently joins the two strands on the footer into a single strand.