Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology

Abstract

Nucleic acid nanotechnology exploits the programmable molecular recognition properties of natural and synthetic nucleic acids to assemble structures with nanometer-scale precision. In 2006, DNA origami transformed the field by providing a versatile platform for self-assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site-specific (spatially addressable) DNA 'staples'. This revolutionary approach has led to the creation of a multitude of two-dimensional and three-dimensional scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy.

Figure 1

Chemical structures of nucleic acids. Nucleotide backbone structures for (a) DNA (left), RNA (right), (b) PNA, and (c) LNA. The right side of panel a also indicates the backbone hydrolysis reaction of RNA, where “AH⁺” and “B” are an acid and base catalyst, respectively. (d) Structure of a double-stranded nucleic acid incorporating the four principal natural nucleobases A, T/U, G, and C, as well as artificial P:Z base pair.

Figure 2

DNA crossover motifs. The (a) double and (b) triple crossover motifs are demonstrated by the red strand.

Figure 3

The DNA origami method. (a) The single-stranded DNA “scaffold” strand (purple) is folded and held in place by specifically hybridizing “staple” strands (red and green). (b) Resultant rectangular origami tile once all the staples have bound to the scaffold. (c) Triple crossover motifs demonstrated by the staples interacting with the scaffold. (d) 5’ ends of the staples are extended to create overhangs, which then can be decorated with partially complementary oligonucleotides (purple).

Figure 4

Current state-of-the-art of nucleic-acid-based nanotechnology. (a) Molecular nanorobot walking along a track generated by decorating a rectangular origami with leg footholds (substrates); below, tile (boxed) imaged using AFM over time, indicating spider movement. (b) Multistep synthesis of an organic compound mediated by a deoxyribozyme. (c) Junctions of carbon nanotubes and origami to create a field-effect transistor. (d) Transfer of photonic energy along a DNA template using FRET. (e) Triangular DNA origami arranged using electron beam lithography. (f) DNA nanotubes arranged using soft lithography. Each panel was reproduced with permission from the respective publisher.

Figure 5

Hierarchy of areas impacted by DNA origami technology. The foundational DNA scaffolds (green) are used to create devices (blue) for a broad variety of applications (orange) that can be combined to enhance numerous emerging interdisciplinary fields (purple). Disclaimer: the nucleic acid nanotechnology field will not be limited by our current vision.

Figure 6

Progression in DNA and RNA nanotechnology. . In nature, DNA forms structures such as the Holliday junction, which has inspired scientists to create more complex structures such as the rectangular DNA-origami tile. In the future, such tiles may be used in fields including nanoelectronics as a scaffold for plasmonic circuit components to generate circuits that mimic neuron behavior. As the simple example in the figure depicts, a new circuit connection (purple) may be strengthened by repeated cooperative stimuli from excitatory pathways (green and blue) and hindered by the stimuli from an inhibitory pathway (orange). In nature, RNA plays a catalytic role in peptide bond formation by the ribosome, arguably the most important enzyme on earth. The catalytic and exquisite molecular recognition activity of RNA is exploited in (deoxy)ribozyme computing, which may be used in the future for complex therapeutic nanomedicine applications. For instance, a drug carrier, specifically delivered to a diseased cell through endocytosis triggered by binding to a protein on the cell surface, opens after entering the cell to release the drug. The contents of the drug carrier include a miRNA mimic that causes repression of a specific protein that otherwise would inhibit the surface marker, resulting in a cell that becomes more receptive to the drug carriers.