DNA Nanostructures in the Fight Against Infectious Diseases

Abstract

Throughout history, humanity has been threatened by countless epidemic and pandemic outbreaks of infectious diseases, from the Justinianic Plague to the Spanish flu to COVID-19. While numerous antimicrobial and antiviral drugs have been developed over the last 200 years to face these threats, the globalized and highly connected world of the 21st century demands for an ever-increasing efficiency in the detection and treatment of infectious diseases. Consequently, the rapidly evolving field of nanomedicine has taken up the challenge and developed a plethora of strategies to fight infectious diseases with the help of various nanomaterials such as noble metal nanoparticles, liposomes, nanogels, and virus capsids. DNA nanotechnology represents a comparatively recent addition to the nanomedicine arsenal, which, over the past decade, has made great progress in the area of cancer diagnostics and therapy. However, the past few years have seen also an increasing number of DNA nanotechnology-related studies that particularly focus on the detection and inhibition of microbial and viral pathogens. Herein, a brief overview of this rather young research field is provided, successful concepts as well as potential challenges are identified, and promising directions for future research are highlighted.

Keywords: DNA nanotechnologies; detection; infectious diseases; inhibitions; nanomedicine; pathogens.

Figure 1

Strategies for the DNA nanostructure‐based detection of nucleic acid biomarkers. a) Dendrimeric fluorescent DNA barcodes. Reproduced with permission.^{[ 62 ]} Copyright 2005, Springer Nature. b) Plasmonic DNA origami nanoantenna for the detection of Zika nucleic acids using FQHs. Reproduced with permission.^{[ 65 ]} Copyright 2017, American Chemical Society. Further permission related to the material excerpted should be directed to the American Chemical Society. c) A switchable DNA origami device carrying AuNRs for the detection of HCV‐specific RNA by CD spectroscopy. Reproduced with permission.^{[ 70 ]} Copyright 2018, John Wiley and Sons. d) Topological DNA origami barcodes for the genotyping of HBV. Reproduced with permission.^{[ 73 ]} Copyright 2018, John Wiley and Sons. e) DNA tetrahedron on a gold electrode for the electrochemical detection of IAV genes using a HRP redox probe. Reproduced with permission.^{[ 74 ]} Copyright 2015, American Chemical Society.

Figure 2

Strategies for the DNA nanostructure‐based detection of protein biomarkers. a) An RCA‐resistant DNA catenane can be activated by a DNAzyme that cleaves an RNA recognition site (blue) incorporated in one of the rings (panel i). The combination of HRCA with a DNAzyme that is activated only in the presence of a certain protein biomarker (panel ii) enables E. coli detection. Reproduced under the terms of the Creative Commons Attribution 4.0 International License.^{[ 75 ]} Copyright 2016, The Authors. b) A DNA tetrahedron carrying a fluorophore quencher close to a hairpin loop modified with an RNA sequence. Hybridization of an ASO enables the cleavage of the loop by HIV RNase H, which restores fluorescence. Reproduced with permission.^{[ 78 ]} Copyright 2019, American Chemical Society. c) An antibody‐modified DNA tetrahedron on a gold electrode for the electrochemical detection of S. pneumoniae‐specific PspA protein using a FeC‐labeled antibody as a redox probe. Reproduced with permission.^{[ 81 ]} Copyright 2017, American Chemical Society.

Figure 3

Strategies for the DNA nanostructure‐based detection of whole pathogens. a) Electrochemical detection of E. coli by antibody‐modified DNA tetrahedra on a gold electrode and FeC‐labeled antibodies as a redox probe. Due to the large size of the bacterium (panel i), charge transport between the probe antibodies and the electrode surface is hindered. This problem does not occur when detecting molecular biomarkers from cell lysate (panel ii). Reproduced with permission.^{[ 82 ]} Copyright 2015, John Wiley and Sons. b) Upon binding of S. aureus, a DNA template is released from aptamer‐modified magnetic beads and multiplied by the interplay of polymerase and endonuclease enzymes. The amplified DNA strands open hairpins and facilitate their assembly into DNA hexagons, which are loaded with an intercalating dye for fluorescence detection. Reproduced with permission.^{[ 83 ]} Copyright 2020, Springer Nature.

Figure 4

Strategies for the delivery of ASOs to bacteria. a) ASOs against the gene ftsZ, critical for replication of MRSA, (panel i) are synthesized from biostable PNA and hybridized on one edge of a DNA‐based tetrahedron nanostructure. (panel ii) Their application to MRSA cells in solution inhibits growth. Reproduced with permission.^{[ 100 ]} Copyright 2018, American Chemical Society. b) A PNA–ASO against three genes responsible for biofilm formation are (panel i) incorporated into a DNA tetrahedron, (panel ii) leading to a decrease of mature biofilm formation, as detected by crystal violet staining and optical density (OD) measurements. Reproduced with permission.^{[ 102 ]} Copyright 2020, Springer Nature.

Figure 5

Strategies for the transport of antibiotics to bacteria by DNA nanostructures. a) The DNA‐binding antibiotic molecule netropsin is loaded into DNA “nanoflower” objects that are formed from a rolling‐circle PCR reaction. Reproduced under the terms of the Creative Commons Attribution 4.0 license.^{[ 104 ]} Copyright 2019, The Authors. b) The antibiotic actinomcycin D intercalates dsDNA and is loaded onto rigid DNA‐based tetrahedron structures. The additional attachment of gold NCs enables concurrent microscopic tracking of the nanostructures. Reproduced with permission.^{[ 106 ]} Copyright 2014, American Chemical Society. c) The positively charged glycopeptide antibiotic VAN is encapsulated within compact “DNA nanogels” formed from the polymerization of small y‐shaped and linear dsDNA monomers. The VAN‐loaded nanogels are surrounded by a protective lipid bilayer to ensure stability in physiological environments. Reproduced with permission.^{[ 107 ]} Copyright 2020, Elsevier B.V.

Figure 6

Transport of peptide‐ and enzyme‐based bactericidal substances. a) An AMP known to disrupt the membrane of several species of bacteria is electrostatically attached to the edges of a DNA tetrahedron. This leads to an enhanced antibacterial rate in species known to be susceptible as well as those that are previously shown to be resistant to the AMP. Reproduced with permission.^{[ 110 ]} Copyright 2020, American Chemical Society. b) A DNA‐based hydrogel is loaded with a broad‐spectrum AMP and used as a wound dressing in in vivo experiments, reducing healing times. Reproduced with permission.^{[ 112 ]} Copyright 2019, Elsevier B.V. c) A bactericidal enzyme, lysozyme, is loaded in high amounts onto a DNA origami nanostructure, together with aptamers that target specific Gram‐negative and Gram‐positive bacteria. Reproduced with permission.^{[ 115 ]} Copyright 2020, John Wiley and Sons.

Figure 7

Current and possible application of DNA‐based nanostructures to fight viral infections. a) The outer surface of the IAV is covered with a large number of HA receptor proteins, which are responsible for binding to host cells. These are homotrimers, comprising three identical subunits. b) Oligonucleotide‐based templates, here a DNA–PNA hybrid, can be used to enable spatially dependent bi‐ or multivalent binding of small ligands (here, a sialic acid derivative known to bind to influenza HA) to targeted virus proteins. (a,b) Reproduced with permission.^{[ 121 ]} Copyright 2017, American Chemical Society. c) The outer surface of the DENV is covered with (panel i) regularly spaced clusters of ED3 receptor proteins. (panel ii) By designing a geometrically complementary DNA nanostructure that bears aptamers that block DENV's ability to infect cells, (panel iii) a high antiviral activity can be achieved, compared with other designs with less similarity to the ED3 cluster distribution. Reproduced with permission.^{[ 124 ]} Copyright 2019, Springer Nature. d) A DNA origami‐based nanovaccine (panel i) is based on the patterning of adjuvants (dsRNA and CpG loops) and tumor antigen peptides onto a stimulus–responsive nanostructure. (panel ii) When injected into living mice, the immune system is stimulated to produce CTLs that attack later challenges with tumor cells. Reproduced with permission.^{[ 92 ]} Copyright 2020, Springer Nature.