Nucleic Acid Enzyme-Based DNA Nanomachine for Biosensing - DNA Nanotechnology: From Structure to Function - page 297

displacement reaction is higher thermal stability of longer DNA duplex over shorter
duplex. Briefly, the strand displacement reaction is initiated by introducing an
external fuel single-stranded (ss) DNA that specifically binds to a recognition site to
a DNA nanostructure. The fuel DNA is then hybridized to the DNA nanostructure
and releases another DNA strand that already hybridized to the DNA nanostructure.
Strand displacement reaction provides a powerful tool by which DNA hybridization
can be employed for DNA devices in a reversible manner. The strand displacement-
triggered DNA machines show high specificity and more motions but usually
generate DNA duplex wastes and have longer response time.
Another promising stimulus to alter DNA sequence in nanostructures is by using
nucleic acid enzymes. Various nucleic acid enzymes may be applied as “nano-tools”
to manipulate DNA. For example, polymerase could “extend” a ss-DNA across
its replication template, while ligase could ligate two ss-DNAs in the presence
of complementary strand. Sequence-specific domains within double-stranded DNA
provide instructive information for the selective binding of endonucleases or nicking
enzymes that catalyze the cleavage of sequence-specific domains and facilitate the
separation of duplex structures. These biocatalytic transformations not only yield
new DNA structures but also generate new versatile components containing sticky
ends that act as secondary assembly units [ 9 ].
Compared with the hybridization or strand displacement-induced mechanical
motion of DNA, nucleic acid enzymes-initiated DNA machines reveal several
advantages. Firstly, nucleic acid enzymes introduce a biocatalytic transformation
that generates more products in one catalytic event compared with the one-to-one
strand displacement reaction. Secondly, since endonucleases or nicking enzymes
possess distinct recognition sites, the direction of the motion could be designed by
rationally embedding the restriction sites in DNA nanostructure. Thirdly, nucleic
acid enzymes could be easily cooperated with other functional nucleic acids, such
as aptamers, DNAzymes, and aptazymes, which offer more functions to DNA
machines. In this chapter, we will focus on the DNA machines triggered by nucleic
acid enzymes and introduce some recent advances in this special field.

14.2 Nucleic Acids Enzyme-Induced Mechanical Motion

of DNA Nanostructure

14.2.1 Ligase and Restriction Enzyme-Assisted DNA Walker

DNA walker is a type of nanomachine made purely from DNA with two single-
stranded “legs” and a DNA track. The “leg” strand is hybridized with the “track”
sequence and could be specifically removed through branch migration. When a
DNA “leg” is lifted from the track in such a way, it can be connected to the next
free foothold strand on the track. This motion could be repeated several times with
the appropriate connector and removal strands to move the walker to an arbitrary