Nucleic Acid Enzyme-Based DNA Nanomachine for Biosensing - DNA Nanotechnology: From Structure to Function - page 299

Tian and Mao used similar principle to generate a system involving a different
kind of unidirectional motion which they termed “molecular gears” [ 12 ]. In this
system, two circular DNA molecules were made to move with respect to each other,
driven by the same mechanism of addition and removal of connector strands. The
two circles consisted of a circular single strand to which three other strands were
hybridized. These strands contained flexible hinges with single-stranded foothold
extensions. The flexibility of the hinges enabled two circles to be linked with two
connector strands simultaneously. By alternating the addition of linker and removal
strands in the correct order, the two circles could then be made to roll against each
other in one direction.

14.2.2 DNAzyme-Assisted DNA Walker

DNAzymes, or deoxyribozymes, refer to some DNA molecules with enzyme-like
catalytic activities [ 13 ]. The first DNAzyme, a 38 nt single-stranded DNA molecule,
which catalyzed the Pb 2C -dependent cleavage of an RNA phosphoester embedded
within a separate DNA molecule, was reported in 1994 [ 14 ]. The cleavage reaction
obeyed Michaelis-Menten kinetics with a multiple turnover kcat value of 1 min 1
at 23 ı C and pH 7.0. The DNAzyme provided a rate enhancement of 105-
fold over the uncatalyzed reaction. Since then, many new DNAzymes have been
reported [ 15 , 16 ], which serve to demonstrate the functional versatility of this
alternative catalytic platform; certain biochemical reactions, such as phosphodiester
cleavage or ligation, can also be catalyzed by RNA or DNA molecules, so-called
(deoxy)ribozymes.
The cleavage or ligation activity of DNAzyme was also employed to drive DNA
walkers. Mao and coworkers have produced a more sophisticated, self-contained
autonomous walker that could constantly walk or rotate from an RNA-cleaving
“10-23” DNAzyme [ 17 ]. The track is a regular, linear array of RNA substrate, S.
The 10-23 DNAzyme contains a catalytic core and two recognition arms that can
bind to an RNA substrate through Watson-Crick base-pairing (Fig. 14.2 a). The two
arms are asymmetrical by design: one arm is 7 bases long and the other is 15 bases
long. When the RNA substrate is cleaved, the short fragment (7-base) dissociates
from the DNAzyme and the long fragment (16-base), in contrast, remains stably
associated with the DNAzyme under the experimental condition (b). After the
short RNA fragment dissociates, the short arm of the DNAzyme becomes unpaired
and can search for other complementary single strands. The RNA substrate next
to the enzyme base-pairs with the short recognition arm of the DNAzyme (c).
The resulting short duplex is stable as a result of intracomplex hybridization.
Following this hybridization, a strand replacement occurs through branch migration,
whereby the intact RNA substrate replaces the cleaved RNA fragment to result
in a more stable, longer, pseudocontinuous DNA duplex (d). In this process, the
DNAzyme moves from one RNA substrate to the next RNA substrate. The process
can be repeated such that the DNAzyme moves continuously. Thus, the DNAzyme
autonomously and processively moves along the track.