Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives

Abstract

DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.

Fig. 1. DNA nanostructures: (A) a double-stranded DNA structure showing hydrogen bonding between two strands. (B) Immobile holliday junction: four single-stranded DNA hybridize based on the sequence complementarity, forming a four-way junction. (C) 2D assembled DNA motifs: double crossover structures, DAE and DAO, and triple crossover DNA (four oligonucleotides chain hybridized into three double-helices) structure. DAE and DAO adapted from ref. with permission. Copyright © 1993, American Chemical Society. TAO Adapted from ref. . With permission. Copyright © 2000, American Chemical Society. (D) 2D self-assembly of DNA star motifs: three-point-star DNA motif assembled forming a two-dimensional hexagonal nanostructure. Adapted from ref. . With permission. Copyright © 2005, American Chemical Society. Cross-shaped DNA self-assembly and a 2D array of DNA motif, six-point-star DNA motif, and a 2D array of motif. Adapted from ref. with permission. Copyright © 2006, American Chemical Society. (E) Dolphin-shaped DNA origami structure: AFM images of the dolphin-shaped DNA origami with different conformational states. Arrows indicate the orientation of the tail as up (u), normal (n), and down (d). Adapted from ref. with permission. Copyright © 2008, American Chemical Society. (F) 3D DNA origami structures: different DNA nanocages constructed as simple wireframe objects with duplex or DX-based edges (left to right: tetrahedron, cube, icosahedron, and buckyball). (G) 3D DNA origami-based motifs; long viral ssDNA folded using DNA staples into DNA origami structures. (H) ssDNA can form mega-Dalton structures as a tile to assemble with other tiles in either 2D or 3D. (I) 2D origami designs from long ssDNA folded by DNA staples. (F–I) reprinted from ref. with permission. Copyright © 2020, American Chemical Society.

Fig. 2. The biological application of DNA nanotechnology in tissue engineering: (a) biological application of different DNA nanomaterials in neural tissue engineering (e.g., TDNs, NPs with pDNA, and polycation with pDNA). (b) The biological application of DNA nanomaterials in skin tissue engineering (e.g., TDNs and polycation/pDNA). (c) The biological application of DNA-based materials in spine tissue engineering. (d) The biological applications of DNA nanomaterials in cardiac tissue engineering (e.g., nanofibrous loaded with pDNA and TDNs). (e) The biological applications of DNA nanomaterials in bone tissue engineering (e.g., TDNs, lipopolysaccharide nanoparticles with DNA, polypeptide-DNA complex, and polycation/pDNA). (f) The biological applications of DNA nanomaterials in muscle tissue engineering (e.g., near-infrared light-activated DNA agonist (NIR-DA) and nanoparticles with DNA).

Fig. 3. Different gateways for cell entry: phagocytosis, micropinocytosis, clathrin-mediated endocytosis, caveola-mediated endocytosis, and clathrin-caveola independent endocytosis.

Fig. 4. DNA nanotechnology for drug delivery: (A) DNA aptamer-drug physical conjugate; a DNA aptamer intercalates with a drug forming a drug-aptamer conjugate. (B) Drug delivery using a DNA nanostructure conjugated with an aptamer: DNA icosahedron formed from a six-pointed star motif conjugated with an aptamer for loading doxorubicin. Adapted from ref. with permission. Copyright 2011 American Chemical Society. (C) DNA carrier–drug complex. (i) Long viral ssDNA scaffold (M13mp18 viral genomic DNA, blue) hybridizes with rationally designed DNA staples, which can fold into different shapes (triangular, square, and tube origami shapes). A breast tumor model was used to investigate the biodistribution of unstructured M13 DNA and different DNA origami nanostructures. The triangle-shaped DNA origami demonstrated optimal tumor accumulation in vivo; it was then used for doxorubicin intercalation. The Watson–Crick base pairs in the double helices of DNA origami serve as docking sites for doxorubicin intercalation (DOX/DNA origami, red). (ii) Tail-injected DOX/DNA origami complexes were transported via blood circulation and owing to EPR effects and were accumulated in nude mouse breast tumours. Adapted with permission from ref. . Copyright 2014 American Chemical Society.

Fig. 5. Immunostimulatory effect of DNA nanomaterials: (A) schematic showing the assembly of CpG-bearing DNA tetrahedron and its immunostimulatory effect. (B) Design of a 30-helix DNA origami tube and endocytic pathway. Different types of CpG-H′s; blue cylinders are double helices DNA nanotubes, and black lines on the tube indicate the possible connection sites for CpG oligonucleotides. DNA origami tube internalized by endocytosis; vesicle segregated by the Golgi apparatus containing the transmembrane toll-like receptor (TLR9); then TLR9 and DNA origami fused with an endosome; recognition of CpG sequence by TLR9 begins the signaling cascade; surface molecules express sand releases cytokines that stimulate further immune response.