DNA nanotechnology assisted nanopore-based analysis

Abstract

Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.

Figure 1.

Schematics of a biological nanopore (A) (33) and a SS nanopore (B) (34). In (A), the target molecule can pass through the pore of α-hemolysin to produce a significant drop in current. The carrier escorting target molecules through SS nanopores induces specific current signals.

Figure 2.

(A) The structure of 2D DNA tile lattices comprising two and four units (62). The images below represent the structures for DAO and DAE units. (B) The original design and AFM images of nanoribbons (69). (C) Schematic drawings of DNA tiles with multiple DNA bridges (73). (D) Schematic drawings and transmission electron microscope (TEM) images of DNA tile assembled 3D nanostructures (77).

Figure 3.

(A) Schematic illustrations of square, rectangle, star, disk with three holes, triangle with rectangular domains, and sharp triangle with trapezoidal domains (78). (B) Direct self-assembly of DNA into nanoscale three-dimensional shapes and TEM results (86). (C) DNA origami nanostructures with complex 3D curvatures (87).

Figure 4.

(A) Schematics of basic DNA strand displacement (90). (B) Catalytic DNA strand displacement circuit where the catalyst DNA can repeatedly participate in multi-cycle reactions (93). (C) Programmable DNA self-assembly pathway based on DNA strand displacement (94).

Figure 5.

(A) Schematic illustration of a synthetic DNA construct assembled using a branched DNA structure translocated through a SS-nanopore (99). (B) SS-nanopore analysis of DNA knot structures (100). (C) Schematics for the SS-nanopore detection of DNA cubes and RNA rings (101). (D) Single-state nanopore analysis of DNAzyme cleavage reaction assisted by DNA tetrahedrons (102).

Figure 6.

(A) Schematic showing analysis of a linear DNA carrier escorting a target molecule nanopore; a 7.2 kbp DNA carrier escorts proteins with different numbers and positions (103). (B) DNA carrier escorting antibody protein to pass through a SS-nanopore (105). (C) DNA carrier escorting dumbbell DNA structures to produce programmable nanopore signals (106). By controlling the numbers and positions of the dumbbell DNA structures, multiple types of specific nanopore signals can be obtained as shown in (D). (E) Protein nanopore screening in human serum using aptamer-modified DNA carriers (56).

Figure 7.

(A) Diagram showing a DNA nanoplate and nanopore. (B) Current trace of a nanoplate-nanopore system. (C) A current–voltage (I–V) characteristic curve of a bare pore and the same pore following successful nanoplate docking (109). (D) Schematic of the ionic current simulation system. (E) Theoretically calculated ionic currents for different bases when translocating the origami hybrid nanopore (110).

Figure 8.

(A) Schematic representation of the DNA origami nanopore (112). (B) Current time curve when a DNA origami nanopore is inserted into a SS-nanopore (112). (C) Schematic of the hybrid nanopore showing the silicon nitride (SiN) membrane (gray) and the DNA nanoplate (red) (113). (D) Typical DNA translocation events for the hybrid nanopore (114). (E) Diagram of the study of a nuclear pore complex based on DNA origami and nanopores (115).

Figure 9.

(A) Schematic illustration and TEM images of the transmembrane channel (120). (B) Design and AFM images of DNA origami nanopores (121). (C) Design of the T-shape pore, composed of a double-layered top plate (gray) and a 27 nm-long stem (red) (122). (D) Synthetic protein conductive membrane DNA nanopore (60).

Figure 10.

(A) Schematic illustrations of the DNA nanopore structure with a valve (57). Fluorophore carboxy-fluorescein (CF, red) and sulpho-rhodamine B (SRB, green) are self-quenched molecules. (B) Fluorescence signals of CF and SRB for vesicles with open valves. (C) Schematic illustration of the DNA nanopore's recognition and endocytosis of a tumor cell (124).

Figure 11.

Schematics of NAND logic gate operations using biological nanopores (A) and the truth table of a nanopore-based NAND gate (B) (127). (C) Bionanopore detections for performing an AND gate using enzymatic reactions (128). (D) Diagram of using a SS-nanopore to verify organized DNA generated in catalytic hairpin assembly and hybridization chain reaction (HCR) DNA circuit reactions (129).

Figure 12.

(A) Schematic diagram of an aptamer-based nanopore sensor for cocaine detection (131). (B) Schematic diagram of cancer detection based on biological nanopores (132). (C) Schematic illustration of the nanopore diagnosis system for small cell lung cancer via detection of miR-20a (133). (D) Schematic illustration of a nanopore sensing strategy based on aptamer binding (134).