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Downloaded 10/8/2021 9:02:16 AM MATERIALS CHEMISTRY FRONTIERS View Article Online REVIEW View Journal | View Issue High-order structures from nucleic acids for biomedical applications Cite this: Mater. Chem. Front., 2020, 4,1074 Alyssa C. Hill * and Jonathan Hall * Over the past 40 years, research in the fields of DNA nanotechnology and RNA nanotechnology has taken nucleic acid molecules out of their biological contexts and harnessed their unique base-pairing and self-assembly properties to generate well-defined, organized, and functional supramolecular architectures. Capitalizing on an intrinsic biocompatibility and the ability to tailor size, shape, and Received 14th October 2019, functionality from the bottom up, recent work has positioned high-order nucleic acid structures as Accepted 23rd January 2020 powerful biomedical tools. This review summarizes advances in nanotechnology that have enabled the DOI: 10.1039/c9qm00638a fabrication of synthetic nucleic acid structures. Nucleic acid-based platforms for biosensing and therapeutic drug delivery are highlighted. Finally, an outlook that considers the limitations and future rsc.li/frontiers-materials challenges for this field is presented. Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Advances in DNA nanotechnology DNA junctions Deoxyribonucleic acid (DNA) is well known as the macromolecule Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zu¨rich, Switzerland. E-mail: [email protected], that encodes genetic information. Taken out of its biological [email protected] context, DNA is also an attractive material for bottom-up This article is licensed under a Alyssa C. Hill graduated in 2013 Jonathan Hall received his PhD with a BS (Summa Cum Laude) in in organic chemistry at Imperial microbiology from the University College in London. He completed Open Access Article. Published on 06 February 2020. Downloaded 10/8/2021 9:02:16 AM. of Oklahoma (USA). She carried post-doctoral work with J.-M. out her PhD at the same Lehn in Strasbourg (FR) and with institution as a National Science Y. Kishi in Cambridge (USA). He Foundation Graduate Research joined the nucleic acids section at Fellow under the supervision of Novartis Pharmaceuticals in Basel Prof. Susan Schroeder. In 2017, in 1992. In the following six years Alyssa began her postdoctoral his group established high- research in the laboratory of throughput oligonucleotide syn- Jonathan Hall at ETH Zu¨rich thesis and genome-wide screening Alyssa C. Hill (CH) with the support of a grant Jonathan Hall using siRNAs. Working with the from the Novartis Research neuroscience department his Foundation (Novartis Forschungsstiftung). Her current work is group developed methods to use siRNAs in vivo which resulted in focused on developing unusually stable viral RNA motifs as therapeutic effects of siRNAs in clinical models of neuropathic pain via nucleic acid-based platforms for therapeutic drug delivery. intrathecal delivery. Jonathan Hall became full professor for Pharmaceutical Chemistry at the ETHZ in 2007. From 2012–2014 he was chair of the Institute of Pharmaceutical Sciences. Jonathan Hall serves on the steering committee of the Drug Discovery Network Zurich (DDNZ), of which he is a co-founder. The long-term objective of his group is to help bring RNA as a target and a drug into mainstream pharma research by making RNA-targeting ligands more drug-like and by identifying new RNA targets that drive disease mechanisms. 1074 | Mater. Chem. Front., 2020, 4, 1074--1088 This journal is © The Royal Society of Chemistry and the Chinese Chemical Society 2020 View Article Online Review Materials Chemistry Frontiers Fig. 1 DNA junctions as units of assembly in extended DNA arrays and discrete DNA topologies. (A) A DNA four-way junction with sticky ends self- assembles into a 2D DNA lattice. (B) A 3D DNA crystal (black) scaffolds proteins (blue) for structure determination by X-ray crystallography. (C) A DNA trefoil knot. (D) Borromean rings made of DNA. (E) A DNA cube. (F) A DNA octahedron. Panels (A) and (B) reprinted from ref. 1 by permission from Springer Nature: Nature Reviews Materials. Copyright 2017. Panels (C–F) reprinted from ref. 14 by permission from Elsevier: Trends in Biotechnology. Copyright Creative Commons Attribution-NonCommercial 3.0 Unported Licence. 1999. fabrication. First, the composition of DNA is known. DNA In the years following Seeman’s innovative proposal, a variety of sequences are made up of four nucleotides: adenine, cytosine, DNA structures were created, including multi-way junctions,6,7 guanine, and thymine (A, C, G, and T, respectively). Second, geometric shapes,8 knots9,10 (Fig. 1C), Borromean rings11 DNA participates in some of the most predictable interactions (Fig. 1D), and polyhedra12,13 (Fig. 1E and F), and thus the field of any natural or synthetic molecule.1 Indeed, DNA sequences of structural DNA nanotechnology was established. form hydrogen bonds according to Watson–Crick base pairing This article is licensed under a rules (i.e., C pairs with G and A pairs with T), and these DNA tiles interactions confer on DNA the capacity for precise molecular While early work in the field of DNA nanotechnology demon- recognition and programmable self-assembly.1,2 Finally, the strated that target topologies could be generated by mani- structure of DNA is defined at the nanometer (nm) scale: pulating flexible junctions, the creation of specific 2- and 3D Open Access Article. Published on 06 February 2020. Downloaded 10/8/2021 9:02:16 AM. DNA helices adopt B-form geometry, with 10.5 base pairs (bp) geometries hinged on the development of more rigid motifs.15 per turn, a diameter of 2 nm, a helical pitch of 3.4 nm, and a To this end, a variety of DNA ‘tiles’ with high structural integrity persistence length of 50 nm.3 However, in nature, DNA exists have been developed.16 One notable example is the double- predominantly as a duplex with a linear helical axis, which is crossover (DX) tile.17 In contrast to the Holliday junction, which poorly suited for fabrication in three dimensions (3D). features one crossover between two DNA duplexes, the DX tile In 1982, Nadrian Seeman conceived of using branched DNA features two crossovers (Fig. 2A). Accordingly, the DX tile has molecules, or junctions, to assemble DNA structures in 2- and a stiffness that is twice that of linear, double-stranded DNA.18 3D.4 Seeman’s inspiration was the Holliday structure, a mobile DX tiles with sticky ends have been shown to self-assemble intermediate of genetic recombination that consists of a single into periodic19 and aperiodic20 2D lattices (Fig. 2A). Further strand exchange, or crossover, between two DNA duplexes. In a research has produced triple crossover (TX)21 and paranemic seminal publication, Seeman proposed rules for constructing crossover (PX)22 tiles, multi-point stars23–25 (Fig. 2B–D), double- immobile DNA junctions from multiple strands and suggested decker tiles26 (Fig. 2E), T-junctions27 (Fig. 2F), Wang tiles,28 and fitting the junctions with ‘sticky ends’.4 Sticky ends are single- other tiles for assembling DNA lattices of varying patterns and stranded overhangs, and cohesion between sticky ends in DNA periodicities, 3D DNA objects with controlled sizes29 (Fig. 2G), generates a helix with standard B-form local geometry.5 By and even DNA-based nano-mechanical devices.30,31 programming DNA junctions to self-assemble via sticky-ended Additionally, in 2009, Seeman’s group used a tile known as cohesion (Fig. 1A), Seeman imagined the creation of extended the tensegrity triangle to produce the first rationally designed, DNA arrays, including 2D lattices and 3D crystals.4 Seeman’s vision self-assembled DNA crystal.32,33 In the tensegrity triangle, seven was that DNA crystals with embedded recognition motifs could be oligonucleotide strands come together to form a structure com- used as hosts to organize proteins and other macromolecule guests prising three struts and three four-way junction vertices, while for structure determination by X-ray crystallography (Fig. 1B).4 two-nucleotide sticky ends mediate self-assembly in 3D (Fig. 2H).32,33 This journal is © The Royal Society of Chemistry and the Chinese Chemical Society 2020 Mater. Chem. Front., 2020, 4, 1074--1088 | 1075 View Article Online Materials Chemistry Frontiers Review Fig. 2 DNA tiles and tile-based structures. (A) Double-crossover (DX) tile (left) and a periodic DNA lattice self-assembled from the DX tile (right). Scale bar: 150 nm. (B) Three-point star motif (left) and a periodic DNA lattice self-assembled from the three-point star motif (right). Scale bar: 50 nm. (C) Four- point star motif (left) and a periodic DNA lattice self-assembled from the four-point star motif (right). Scale bar: 50 nm. (D) Six-point star motif (left) and a periodic DNA lattice self-assembled from the six-point star motif (right). Scale bar: 50 nm. (E) Double-decker tile (left) and a periodic DNA lattice self- assembled from the double-decker tile (right). Scale bar: 200 nm. (F) T-junction (left) and a periodic DNA lattice self-assembled from the T-junction Creative Commons Attribution-NonCommercial 3.0 Unported Licence. (right). Scale bar: 25 nm. (G) Cryo-electron microscopy (cryo-EM) reconstructed models of DNA polyhedra self-assembled from the three-point star motif. Top panel: DNA tetrahedron, middle panel: DNA dodecahedron, bottom panel: DNA buckyball. Scale bars: 5 nm, 20 nm, and 20 nm, respectively. (H) Tensegrity triangle (left) and DNA crystals self-assembled from the tensegrity triangle (right). Scale bar: 500 mm. Panel (A) tile reprinted from ref. 41 by permission from Springer Nature: Methods in Molecular Biology. Copyright 2005. Panel (A) lattice reprinted from ref. 19 by permission from Springer Nature: Nature. Copyright 1998. Panel (B) reprinted with permission from ref. 24. Copyright 2005 American Chemical Society. Panel (C) from ref. 23.
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