Design, Fabrication, and Applications of DNA Nanomachines - DNA Nanotechnology: From Structure to Function - page 219

Keywords DNA nanomachine • i-motif • G-quadruplex • Tweezer • Walker •
Rotor • DNA origami

11.1 Introduction

The main tasks for an efficient molecular machine system include the construction
of scaffolds, the generation of mechanical motions or forces that respond to
certain stimuli, and the capability of monitoring the responsiveness. The unique
molecular recognition and mechanical properties make DNA molecules one of the
best candidates for artificial molecular machines. Besides its main function as the
carrier of genetic information that is encoded by the sequence of four bases (A, T, C,
and G), DNA is a biopolymer with exciting physicochemical properties that can be
influenced by environmental condition or the base composition in various manners.
DNA and its derivatives have been demonstrated as powerful building blocks for
the assembly of the nanostructures with desirable shapes and geometries. Started
by Nadrian C. Seeman [ 1 - 5 ], the structural DNA nanotechnology has enabled
the scientists to prepare complex and intricate DNA crystalline nanostructures
with high yield. The Watson-Crick base-pairing rules of A-T and C-G lead to
the formation of duplex DNA structures, and specific sequence DNA such as
C-rich or G-rich strands tend to form quadruplex structures [ 6 - 8 ]. Meanwhile,
supramolecular DNA nanostructures can be induced in the presence of metal
ions [ 9 ]. Furthermore, diverse structural patterns of DNA based on base-pairing
principles have been built from two-dimensional extended nanostructures to three-
dimensional self-closed nanostructures, from infinite extension to all directions
to the well-defined shape and scale. Especially, the appearance of DNA origami
initiated a “revolution” for the moderate-resolution ( 6 nm) organization of DNA
information into one, two, and even three dimensions [ 10 ]. The origami, developed
by Paul Rothemund, through folding of a long single-stranded viral DNA aided by
multiple smaller “staple” strands, can result in various shapes including a smiley
face [ 11 ] and a coarse map of China [ 12 ], along with many three-dimensional
structures, such as nanotubes [ 13 ], locked/unlocked box [ 14 ], reconfigured m obius
strip [ 15 ], and even 3D spherical shells [ 16 ], ellipsoidal shells [ 16 ], and nanoflask
[ 16 ]. The structural DNA nanotechnology provides the significant fundamentals
for building DNA machines. The specific recognition of DNA to the homo/hetero
molecules, and to various ions, makes it also an ideal material for construction of
sensing device.
Therefore, the technology of assembling the scaffold, the sensitivity to the
environmental change, and the dynamic functions together with the automated
synthesis of DNA strands make DNA well qualified for versatile functional
molecular machines. If the multiplex sensing feature of nucleic acid structures is
integrated with the energetically favored directional migration of nucleic strands,
more complex operation can be implemented in a multimachinery system, such
as interunit cooperation, or cascade activation. However, as a research object,