Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 221

Single-stranded DNA and double-stranded DNA act differently in mechanical
properties, especially in elasticity. The persistence length of dsDNA is 50 nm,
or 150 bp [ 18 ], while the values for ssDNA are between 0.75 nm at high ionic
strength and up to 10 nm at low salt conditions [ 19 ]. Accordingly, single-strand
molecules are considered to be relatively flexible in buffer conditions and double-
strand molecules stiff. So in nanodevice design, single strands usually act as the
parts of flexible joints and hinges, whereas double strands as stiff “arms” or “limbs.”
A sticky end occurs when one strand of the duplex DNA extends for several unpaired
bases beyond the other. Sticky ends are widely used for recognition properties and
assembly of two or more DNA structural units. Hairpin, a single-stranded stem-
loop DNA structure, is the key of the operation principle of many DNA devices,
on account of precise control over the stability and switching kinetics of hairpin
stems.
Homopolymeric DNA can form different unusual conformations involving non-
Watson-Crick base pairing. A-rich DNA has been reported to form parallel duplexes
called A-motifs; C-rich DNA sequences can form i-tetraplex, i-motifs [ 67 ]; and
G-rich DNA sequences can form G-quadruplex [ 8 ]. The topological transitions of
the i-motifs and G-quadruplex induced by environment conditions make them the
important parts on many DNA devices to provide energetic changes or functional
units. Crossover is the genetic event that occurs during gene recombination: two
pieces of DNA duplex break and partially unravel and form four-strand structure.
This structure is utilized to make conformational changes in DNA nanodevices.
Aptamers and DNAzymes are nucleotides with binding specificity and catalytic
activities. An aptamer is a nucleic acid sequence that is typically 15-40 nu-
cleotides or longer and binds specifically to a given molecular target [ 20 , 21 ].
DNAzymes and RNAzymes are metal-ion-dependent catalytic DNA-based enzymes
that have been shown to be capable of catalyzing a variety of chemical reactions
[ 22 - 24 ]. Both aptamers and DNAzymes are of high interest in the context of
information processing, signal transduction, and biosensing. Therefore, utilizing
aptamers and DNAzymes as building blocks paves the way to functional DNA
nanodevices.

11.3 DNA Nanomachines

For any kind of machine, the generation of forces and motions is the key task
to make the machine work. Therefore, it is important to explore various fueling
mechanisms that precisely control the motion of DNA nanomachines. According to
the reported DNA nanomachines, the typical fuels include metal ions, pH, photons,
and DNA strands. Correspondingly, we sort DNA nanomachines into two categories
by their original driving mechanisms.