DNA nanotechnology provides one of the few ways to form designed, complex structures with precise control over nanoscale features. The field is beginning to see application to solve
basic science problems in
structural biology and
biophysics. The earliest such application envisaged for the field, and one still in development, is in
crystallography, where molecules that are difficult to crystallize in isolation could be arranged within a three-dimensional nucleic acid lattice, allowing determination of their structure. Another application is the use of
DNA origami rods to replace
liquid crystals in
residual dipolar coupling experiments in
protein NMR spectroscopy; using DNA origami is advantageous because, unlike liquid crystals, they are tolerant of the detergents needed to suspend
membrane proteins in solution.
DNA walkers have been used as nanoscale assembly lines to move nanoparticles and direct
chemical synthesis. Further, DNA origami structures have aided in the biophysical studies of
enzyme function and
DNA nanotechnology is moving toward potential real-world applications. The ability of nucleic acid arrays to arrange other molecules indicates its potential applications in molecular scale electronics. The assembly of a nucleic acid structure could be used to template the assembly of a molecular electronic elements such as
molecular wires, providing a method for nanometer-scale control of the placement and overall architecture of the device analogous to a molecular
 DNA nanotechnology has been compared to the concept of
programmable matter because of the coupling of computation to its material properties.
In a study conducted by a group of scientists from
CDNA centers in
Aarhus University, researchers were able to construct a small multi-switchable 3D DNA Box Origami. The proposed nanoparticle was characterized by
atomic force microscopy (AFM),
transmission electron microscopy (TEM) and
Förster resonance energy transfer (FRET). The constructed box was shown to have a unique reclosing mechanism, which enabled it to repeatedly open and close in response to a unique set of DNA or RNA keys. The authors proposed that this "DNA device can potentially be used for a broad range of applications such as controlling the function of single molecules, controlled drug delivery, and molecular computing."
There are potential applications for DNA nanotechnology in nanomedicine, making use of its ability to perform computation in a
biocompatible format to make "smart drugs" for
targeted drug delivery. One such system being investigated uses a hollow DNA box containing proteins that induce
apoptosis, or cell death, that will only open when in proximity to a
 There has additionally been interest in expressing these artificial structures in engineered living bacterial cells, most likely using the
transcribed RNA for the assembly, although it is unknown whether these complex structures are able to efficiently fold or assemble in the cell's
cytoplasm. If successful, this could enable
directed evolution of nucleic acid nanostructures.
 Scientists at
Oxford University reported the self-assembly of four short strands of synthetic DNA into a cage which can enter cells and survive for at least 48 hours. The fluorescently labeled DNA
tetrahedra were found to remain intact in the laboratory cultured human
kidney cells despite the attack by cellular
enzymes after two days. This experiment showed the potential of drug delivery inside the living cells using the DNA ‘cage’.
 A DNA
tetrahedron was used to deliver
RNA Interference (RNAi) in a mouse model, reported a team of researchers in
MIT. Delivery of the interfering RNA for treatment has showed some success using
lipid, but there are limits of safety and imprecise targeting, in addition to short shelf life in the blood stream. The DNA nanostructure created by the team consists of six strands of DNA to form a tetrahedron, with one strand of RNA affixed to each of the six edges. The tetrahedron is further equipped with targeting protein, three
folate molecules, which lead the DNA nanoparticles to the abundant
folate receptors found on some tumors. The result showed that the gene expression targeted by the RNAi,
luciferase, dropped by more than half. This study shows promise in using DNA nanotechnology as an effective tool to deliver treatment using the emerging RNA Interference technology.