1. Introduction

Nanophotonics is an emerging hot area that aims to investigate the behavior of light on the nanometer scale, as well as to understand and utilize the interactions between light and nanometer-sized objects. It has been well known that the optical properties of nanophotonic systems are highly dependent on their morphology, including size, shape and spatial relationship of all the functional units [1–3]. As a result, extensive efforts have been spent on the development of advanced fabrication technologies to create nanophotonic structures with well-defined nanometer scale structural patterns, which may display desired optical or spectroscopic properties, leading to various novel applications.

In general, the methods used for nanometer scale patterning can be classified into top-down and bottom-up methods. Top-down techniques involve a series of lithographical approaches such as photolithography (PL) [4], electron-beam lithography (EBL) [5], as well as various templated fabrication strategies [6–8]. These methods rely on miniaturizing or breaking down bulk materials to create nanomaterials, or by selectively removing part of a bulk material to generate nano-patterns and nano-features. In contrast, bottom-up methods build up desired nanostructures from controlled growth or self-assembly of individual molecules and particles. Conventional bottom-up patterning strategies include colloidal lithography, sol-gel method, additive manufacturing, etc. [9–12].

Despite of the vast number of applicable patterning techniques, significant limits still exist to meet all the requirements in modern nanophotonics. The best spatial resolution in nanofabrication, for example, can rarely go down to 10–20 nm, which is insufficient to make ultra-small nanogaps for reliable investigation of quantum optical phenomena [13,14]. In addition, it is difficult to create three dimensional (3D) asymmetric or chiral nanostructures. Most top-down and bottom-up techniques are based on homogeneous driven force, which intrinsically lacks the ability to break symmetry [15,16]. Finally, the deterministic insertion of emitters at the center of an already formed nanostructure is extremely challenging [17,18]. It is essentially impractical to use mechanical or lithographic alignments (i.e. top-down methods) to achieve reproducible and accurate placement of individual emitters in any pre-formed nanogaps.

DNA origami enables a number of novel bottom-up strategies to fabricate nanophotonic structures that are not feasible by conventional nanofabrication methods. The Japanese word “origami” means paper folding. In a typical experiment, hundreds of short “staple” DNA strands are programmed to fold a long single-stranded “scaffold” strand into designed shape, following a pre-determined routing path (Fig. 1(a)) [19–21]. As both the base pairing rules and spatial geometry of DNA double helix have relatively high fidelity [22], the morphology of DNA origami is generally predictable [19]. A series of open access tools have already been developed, including cadnano, nanoengineer, Parabon inSēquio, Tiamat, etc., to assist the design of DNA origami and to predict the final structure of the assembled products [23–26]. By programming the sequences of the staple strands properly, a wide variety of 2D and 3D DNA structures have been successfully synthesized [19,27], demonstrating the outstanding morphological tunability of DNA origami.

 

Fig. 1. Working principles of DNA origami formation and decoration. (a) Scheme of the DNA origami technique. A long strand of DNA (black, called scaffold strand) is folded according to a designed folding path by binding with a set of short DNA strands (colored, called staple or helper strands). Both 2D and 3D structures can be created. Reproduced with permission from Ref. [21]. Copyright (2018) American Chemical Society. (b) A representative scheme showing the bonding between DNA origami and other substances at desired sites and their immobilization on a substrate for optical measurement. Reproduced with permission from Ref. [32]. Copyright 2012, AAAS.

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Not only does DNA origami secure high freedom and accuracy in self-assembly processes, it also holds great compatibility with various materials, organic or inorganic. Modern organic chemistry enables chemical modification of a DNA strand at almost arbitrary positions, either on the backbone or on the base [28–30].The modified DNA molecules can interact with a diversity of substances, including ions, molecules, proteins, metallic nanoparticles and semiconductor nanoparticles, to yield DNA-containing hybrid materials, which may be selectively decorated at desired locations of DNA origami (Fig. 1(b)) [31,32] with spacing along the DNA helices as small as 0.34 nm (generally 3.4–7 nm) and perpendicular to the DNA helices about 0.5–5 nm (generally 2.5–5 nm). These merits make DNA origami an ideal tool for constructing nanophotonic structures.

It is worthwhile to note that the actual structure of DNA origami may be different from the expected one in the design, due to subtle deviations of the number of base-pairs per DNA helical turns used in the design, from that of the natural twist of DNA in the unconstrained state, which causes a compensating global twist and bending of the final structure in response to the structural constrain [33]. This global deformation may be corrected in some extend by using a design that is closer to the natural twist of DNA (i.e. 10.5 bp per turn in the cases of 21 bp per two turns = 7 bp per 2/3 of a turn, vs. 10.67 bp per turn in the cases of 32 bp per three turns = 8 bp per ¾ of a turn), or by adding or deleting some base-pairs at certain sites.

In addition, some significant morphological deformations have been witnessed when the ionic strength of solution has changed, or when the DNA origami is dried in air [34,35]. To overcome those issues, a couple of strategies have been devised to improve the structural stability of DNA origami. Sol-gel chemistry was employed to deposit a layer of silica on the DNA origami [35,36]. The as-treated DNA structures exhibited greatly enhanced structural stability, which maintained their original geometries under mechanical stress or harsh chemical conditions. Besides, peptide coating has been utilized in Gang and Shih groups to protect DNA nanostructures from low-salt denaturation and nuclease degradation to improve their biocompatibility [37,38].

To date, a number of examples of DNA origami-enabled assembly of nanophotonic structures have been demonstrated. In this review, we introduce a series of frontier works that represent the state of the art of this fast developing field. The design principle, critical assembly strategies and representative achievements are discussed briefly. Utilizing DNA origami as template for nano-patterning have led to many unique applications in plasmonics, optics and sensing devices. We will go through several examples in each of these directions to show that DNA nanotechnology could out-perform the traditional nano-patterning methods in construction of nanophotonic devices.

Many decent reviews and perspectives on DNA origami nanophotonics were very recently published [21,31,39]. Compared with these outstanding reviews, we employ a more straightforward classification to introduce various photonic structures. Zero-, one-, two- and three-dimensional nanophotonics formed via DNA origami-mediated assembly are reviewed first, following the order of their morphological complexity. Notably, we also include some examples of metal-nanoparticle-free photonic structures, which were usually neglected in the previous reviews.

2. DNA enabled assembly of nanophotonic structures

2.1 Nanocavities

Nanocavities, such as nanogaps, nanowells, etc. are one of the simplest nanostructures that have been used to trap light [40]. Strong light confinement via different resonating modes at wavelength or sub-wavelength scales has been witnessed by previous research, which plays a key role in lasing, non-linear optics and quantum optical studies [40,41]. A more prominent field is to construct hybrid nanophotonic systems using nanocavities and single emitters. Fluorophores or quantum dots placed in nanocavities can interact with the strongly localized optical fields and show enhanced or altered optical properties [42,43].

To reliably build such systems, it is necessary to achieve both high resolution in nano-patterning, as well as the deterministic placement of emitters in the cavity. In another word, the fabrication technique should allow a well-defined number of optically active components to be positioned at specific locations with an error that is orders of magnitude smaller than the wavelength of light.

The above criterions can be readily satisfied by using DNA origami mediated self-assembly. By extending single-stranded docking DNA, the DNA origami is able to bind emitters modified with the complementary DNA strands. The number and location of the bound emitters can be well controlled by the number and distribution of the docking strands extending from the DNA origami. Such a DNA origami-emitter complex can be further integrated into optical nanocavities, yielding interesting nanophotonic devices.

Gopinath et al. has demonstrated tunable nanocavity emissions with the help of DNA origami [44]. A triangular DNA origami was modified with a number of Cy5 fluorescent dyes and attached to a photonic crystal cavity (PCC) through pre-defined electrostatic binding sites (Fig. 2(a)–2(b)). By controlling the relative position of the origami binding site within the cavity, the fluorescent dyes decorated on the DNA origami located within the PCC exhibited a tunable emission intensity, responding to the spatial distribution of the electric field intensity within the cavity. The optimum intensity was observed when the DNA origami dwelled at one of the seven strongest antinodes of the cavity. It had also been found that the emission intensity was proportional to the number of DNA origami inside the cavity, as well as the number of dyes on each origami. Combining all those tools, researchers replicated Van Gogh’s The Starry Night with 65,536 cavities, demonstrating the ability to rapidly prototype a broad array of hybrid nanophotonic devices (Fig. 2(c)). Recently, the same group demonstrated absolute and arbitrary alignment of single-molecule in PCC by DNA origami [45]. By tuning the relative angle between the dipole of fluorescent dyes and the polarization of the incident light, the device brightness could be controlled.

 

Fig. 2. DNA origami assisted tuning of emissions in nanocavities. (a) The structure of Cy5 modified DNA origami. Scale bars: 50 nm. (b) Location dependent emission of in Cy5 modified DNA origami a PCC. Scale bars: 250 nm. (c) Van Gogh’s The Starry Night realized with an array of nanocavities. (d) A nanocavity formed by a pair of AuNPs. Scale bar: 200 nm. (e) The polarization dependent emission pattern of the nanocavity in (d). (a)-(c) Reproduced with permission from Ref. [44]. Copyright (2016) Springer Nature. (d)-(e) Reproduced with permission from Ref. [46]. Copyright (2019) American Chemical Society.

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Beside intensities, the polarization of single-molecule emission may also be manipulated via DNA origami assembled nanocavities. An optical antenna composed of two colloidal gold nanoparticles (AuNPs) separated by a ∼13 nm gap was fabricated using a planar DNA origami, in which a single Cy5 fluorophore was placed near the gap center (Fig. 2(d)) [46]. The system exhibited a polarization-dependent emission pattern, which was mediated by the main resonant mode of the cavity (Fig. 2(e)). The fluorescent lifetime and emission intensities were also shown to vary with the direction of the polarization.

One of the most promising applications of DNA origami assembled nanocavities is the study of strong coupling. A large coupling strength (g) between an emitter and an optical cavity results in mixed states that is half-light, half-matter, which can be usually told by an anti-crossing behavior in the spectrum known as Rabi energy splitting [13].

For a nanocavity formed by lossy materials in dielectric medium, its mode volume (V) can be calculated by the following equation:

To realize strong coupling under room temperature, it is required that the V of nanocavities should be well below 10⁻⁶ λ³ in order to suppress emitter scattering and energy loss [47]. This typically corresponds to a cavity size of about 10⁻² λ in each dimension, where λ is the incident light wavelength. In the visible light regime, such a scale is too small to reach by conventional patterning methods, but this can be easily accomplished by DNA nanotechnology.

In one example, a nanocavity with mode volume of approximately 200 nm³ was fabricated with surface coupled nanospheres [48,49]. A fluorophore containing DNA origami was sandwiched between a AuNP and a plasmonic substrate, leading to a sub-5 nm optical cavity (Fig. 3(a)). Clear Rabi splitting was observed from the scattering spectrum of the system. By varying the lateral position of the molecule in the gap, the spatial profile of the local density of optical states could be directly mapped.

 

Fig. 3. DNA origami templated strong plasmon-exciton coupling studies. (a) Surface coupled nanospheres and their spectra. Reproduced with permission from Ref. [48]. Copyright (2018) American Chemical Society. (b) AuNP dimers for strong exciton-plasmon coupling tests. Scale bars: 50 nm. Reproduced with permission from Ref. [50]. Copyright (2016) American Chemical Society. (c) A nanocavity formed by AuNRs in a tip-to-tip configuration and corresponding spectral characterizations. Reproduced with permission from Ref. [52]. Copyright (2021) Springer Nature.

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Roller et al. assembled AuNPs on both sides of a planar DNA origami to achieve nanometer-sized interparticle spacing [50]. The plasmon resonance of such nanocavities might be adjusted by varying the nanoparticle diameter while keeping their separation distance constant. After absorbing J-aggregates on the DNA origami sitting between the AuNPs, the scattering profile of the gold nanoparticle dimer showed obvious energy splitting, indicating the presence of strong plasmon-exciton coupling (Fig. 3(b)). A similar idea had been demonstrated by Zhu et al. in which two gold nanorods (AuNRs) were placed on the opposite sides of an origami to create chiral plasmonic-excitonic coupling [51], manifested by a large Rabi splitting and anti-crossing behavior in the circular dichroism spectra.

Recently, our group devised a strategy to assemble AuNRs in a tip-to-tip fashion into ultra-small nanocavities [52]. A saddle-shaped DNA origami with two tubular grooves was synthesized, which geometrically aligned two AuNRs in a linear configuration with a gap as small as 2–3 nm and a bending angle <10° (Fig. 3(c)). By changing the aspect ratio (AR) of the AuNRs, the resonant frequency of the plasmon system could be tuned in a broad range. An obvious energy splitting was witnessed when a Cy5 molecule was placed into the nanocavity, the magnitude of the energy splitting observed was among the best recorded values.

2.2 Asymmetric and chiral structures

Introducing symmetry breaking may result in many interesting phenomena in optical systems. Fano resonance, for example, has been discovered in a number of asymmetric plasmonic structures and is well known for its unique asymmetric spectral line-shape [3,53]. Among the whole library of asymmetric features, chirality is one of the most fascinating motifs. A chiral or handed structure cannot be superimposed with its mirror image, which has profound influences on the optical properties [54,55].

Fabricate asymmetric features by conventional self-assembly techniques, such as colloidal lithography [3] and molecular self-assembly [56], is not an easy task. The energy flow (e.g. heat, light, etc.) and material flow (e.g. movement of particles) in those methods are highly isotropic thus cannot yield symmetry breaking.

Due to its superior patterning ability, DNA origami is an ideal tool to construct asymmetric nanostructures, which are usually clusters of nanoparticles, or a 1D chain of particles [57–60]. For instance, anisotropic plasmonic gold nanostructures may be assembled by using a DNA-origami-based precise machine to transfer essential DNA sequence to the surface of AuNRs [61]. The transferred sequences maintained their original spatial configurations on the origami, which could align DNA coated nanoparticles in a highly specific manner. Distinct hybrids of AuNPs and AuNRs were fabricated with such method. Recently, Yao et al. developed a jigsaw-puzzle-like assembly to obtain super-origami nanostructures. Oligonucleotide-functionalized AuNPs were applied as universal joint units for a one-pot assembly of triangular DNA origami [62]. Unique asymmetric hybrid materials had been created (Fig. 4(a)). The AuNPs anchored at predefined positions exhibited strong interparticle coupling, leading to the emerging of multiple plasmonic peaks.

 

Fig. 4. DNA origami enabled asymmetric and chiral structures. (a) Asymmetric patterns assembled by jigsaw-puzzle-like strategy. Reproduced with permission from Ref. [62]. Copyright (2015) Wiley-VCH. (b) Chiral AuNP tetramers. Reproduced with permission from Ref. [66]. Copyright (2013) American Chemical Society. (c) Reconfigurable 3D plasmonic metamolecules. Reproduced with permission from Ref. [78]. Copyright (2014) Springer Nature. (d) Tunable chiral chains of gold nanorods. Reproduced with permission from Ref. [79]. Copyright (2017) Wiley-VCH.

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Fabricating chiral structures with DNA origami has been drawing a lot attention [63,64]. The pioneering work in this field was accomplished in 2012 by Liedl and Govorov [65]. After that, various chiral structures were obtained by positioning metal nanoparticles or nanorods on both sides of planar DNA origami to achieve a chiral configuration. For example, Shen et al. assembled a 3D tetramer using four different sized AuNPs that displayed plasmonic chirality (Fig. 4(b)) [66]. It was also possible to integrate gold-silver core-shell plasmonic nanorods to get chiral structures with strongly increased circular dichroism (CD) signal [67]. Using DNA origami as a precise spacer, it has been found that the chirality in plasmonic nanostructures can be transferred over distances up to 100 nm [68]. On the other hand, inserting transmitter particles greatly enhances the CD response, regardless whether the transmitter is chiral or achiral. This phenomenon is attributed to the near-field coupling among plasmonic nanoparticles.

One of the most attractive features of DNA-origami assembled chiral structures lays in its dynamic, responsive capability [59,69,70]. Many external stimuli, such as pH, light and oligonucleotides, can trigger the dissociation or rearrangement of DNA origami structure, leading to reconfigurable optical behavior [71–75]. Jiang et al. developed responsive hinges to connect two DNA origami-bound AuNRs to form chiral nanostructure [76]. A hinge containing a disulfide bond that might be broken by adding a specific reducing agent, like glutathione, leading to the disappearance of CD. DNA origami with hinges containing DNA i-motif or azo-functional group could undergo reversible geometric change in response to a pH change or UV light and generate controllable CD responses. This property has been employed in sensor designs and is covered in session 3.4. Similar idea has been utilized to modulate surface attached responsive chiral units [77]. By changing the configuration of two DNA anchors, the chiral structure might be switched between a perpendicular and a parallel state respect to the incident light polarization, thus yielding variable CD signals.

In fact, the DNA based chiral system could possess several distinctive states, the interchange of which may be regulated by a combination of fuel and set DNA strands [78]. As shown in Fig. 4(c), the adding of DNA fuel strands altered the chirality of the AuNR pair in a stepwise manner. Each state can be reproduced after a full cycle. Recently, our group also developed a couple of novel designs of tunable chiral structures [79,80]. Here a V-shape origami was applied to tune the chiral structure. The open angle of each individual V-shaped origami, or the relative angle of adjacent DNA origamis were modulated through adding specific DNA sequences, which rendered reconfigurable CD signals (Fig. 4(d)).

2.3 2D patterns and arrays

DNA origami is also capable of patterning 2D features and planar nanostructure arrays [81–83]. DNA molecules are negatively charged in common buffers, which possess good affinity with positively charged surfaces themselves, or negatively charged substrates under the presence of multivalent cations [44]. As a result, DNA bound nanoparticles can be effectively delivered to desired surficial locations through Columbic interactions. The surface is usually pre-treated with EBL or other lithographical methods to yield charged patterns that accommodate the size and shape of DNA origamis [84]. Alternatively, specific interactions between biomolecules could also be applied for DNA origami attachment. For example, Pibili et al. realized single-molecule positioning in neutravidin coated zero-mode waveguides with biotin functionalized DNA origami nano-adapters [85]. Each DNA origami was geometrically tailored to fit the shape of nanowells on the surface (Fig. 5(a)), leading to precise control of the number and location of functional molecules inside each cavity.

 

Fig. 5. 2D patterns assembled by DNA origami. (a) Single-molecule positioning in zeromode waveguides by DNA origami. Reproduced with permission from Ref. [85]. Copyright (2014) American Chemical Society. (b) 2D metal particle arrays assembled by DNA origami. Scale bars: 200 nm. Reproduced with permission from Ref. [86]. Copyright (2016) Springer Nature. (c) DNA origami templated metal growth. Scale bars: 100 nm. Reproduced with permission from Ref. [89]. Copyright CC BY 4.0.

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DNA origami could also be designed to self-assemble into different geometric patterns, which in turn generated assorted DNA-framed nanoparticle arrays (Fig. 5(b)) [86,87]. The binding between nanoparticles and DNA docking strands immobilized on a surface was shown to be affected by the density of docking strands [88]. A high density of docking strands led to the preferential binding of smaller nanoparticles, which maximized the number of DNA base pairing. In contrast, smaller nanoparticles were not able to form effective multivalent binding with DNA docking strands of lower density. In such a case, larger particles tend to associate more preferably with DNA structures.

Except being a nanoparticle carrier, surface anchored DNA origami could also act as templates for seeded metal growth [89]. Jin et al. utilized immobilized DNA origami to fabricate metal-coated DNA patterns that of a few nanometer thickness and reassemble the size and shape of the underlying DNA origami (Fig. 5(c)). Those patterns might serve as masks to further transfer their structural patterns onto the substrate layers through physical or chemical etching.

DNA origami may also serve as hard masks for surface patterning. Hui et al. applied DNA-inorganic hybrid structure to achieve deep etching of a Si wafer for antireflection applications [90]. Diagne et al. directly used bare DNA origami as masks in silica etching [91]. The results demonstrated the great potential of DNA origami in lithographical applications.

2.4 Macroscopic and mesoscopic 3D photonic materials

DNA origami is capable of building 3D nanostructures with high freedom and accuracy. In fact, several of the works mentioned in the previous sections already involved DNA-origami assembled 3D nanophotonics [66,79,80]. However, those systems only contained individual nano-sized structures, which are far from being a real 3D material.

Great efforts had been spent on extending the patterning capability of DNA origami into macroscopic and mesoscopic photonic materials. A few examples have achieved 3D photonic structures of at least 10 µm in scale. The most straightforward idea of constructing 3D DNA structures is to accumulate 3D DNA origami units in a periodic pattern. Zhang et al. employed beam-shaped DNA origami blocks to create crystals up to a few tens of micrometers [92]. Three 14-helix bundles of equal lengths were interconnected at defined positions to form a rigid and constrained tensegrity triangle structure, which could be linked at all ends to neighboring units to form periodic rhombohedral crystalline lattices containing 90% v/v empty space (Fig. 6(a)). The lattice constant was approximately 50–60 nm. AuNPs were further incorporated at the connecting points to fabricate a 3D AuNP array (Fig. 6(b)), which could be of great potential in plasmonic applications.

 

Fig. 6. 3D photonic structures assembled by DNA origami. (a) A protocol to prepare DNA origami single crystals. (b) Inserting metal nanoparticles into the crystal lattice in (a). Scale bars: 500 nm. (a)-(b) Reproduced with permission from Ref. [92]. Copyright 2018 Wiley-VCH. (c) Synthesizing DNA origami crystals using octahedral DNA frames. Scale bars: 2 µm. Reproduced with permission from Ref. [93]. Copyright CC BY 4.0. (d) Inserting nanoparticles inside octahedral DNA frames. Reproduced with permission from Ref. [94]. Copyright (2020) American Chemical Society. (e) Building DNA origami crystals with rods connected octahedrons. Reproduced with permission from Ref. [95]. Copyright (2021) American Chemical Society. (f) Micron-sized DNA spiral ribbons assembled from DNA filaments. Scale bars: 2 µm. Reproduced with permission from Ref. [96]. Copyright (2017), Springer Nature.

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Octahedral DNA origami frames have also been applied to fabricate single crystalline assembly [93]. By regulating the symmetries and binding modes of the DNA octahedron, the crystalline shapes could be designed and well-controlled (Fig. 6(c)). It is possible to insert nanoparticles inside the octahedral frames as a guest [94], which would lead to the formation of 3D lattice of nanoparticles (Fig. 6(d)). Ma et al. slightly modified this strategy and connected octahedral DNA frames with rigid DNA rods [95]. The resulting products were more porous and robust, whose lattice constant could reach about 74 nm (Fig. 6(e)).

In addition to creating rigid solid crystals, studies have also been carried out on fabricating liquid crystals (LCs) with DNA origami. Recently, the molecular engineering of chiral colloidal LCs using DNA origami has been demonstrated [96,97]. DNA origami filaments were synthesized and further self-assembled into micron-long twisted ribbons, which formed LC phases when incubated with non-adsorbing polymer solutions (Fig. 6(f)). By mixing two different types of DNA filaments, the handedness of the final products could be tuned.

To obtain photonic crystals that can work under visible wavelengths, it is necessary to increase the lattice constant to a few hundred nanometers [98]. Due to the intrinsic scale of a single DNA origami, there exists a size limit for single-origami building blocks [99]. To breakthrough this limit, giant building units composed of multiple DNA origamis could be employed. It was demonstrated that a giant DNA origami tetrapod could be assembled from 6 individual DNA origamis [100]. This unit could further self-assemble into macroscopic networks. The as-formed diamond-like photonic crystals had much greater lattice constant and photonic bands in the visible regime, which might possess potential for practical applications.

Although the above strategy allows for making macroscopic and mesoscopic 3D photonic materials, the fabrication cost is too high for practical applications [96], a more cost-effective way is to mix DNA origami with other cheaper materials [101]. Martens et al. showed that when AuNP decorated DNA bars was mixed with a lyotropic chromonic LC, they might be uniformly aligned with proper substrates [102]. This promising result is likely to open a new route toward making bulk materials with anisotropic plasmonic properties. In another example, photo-switchable chiral DNA-origami colloidal nanostructures was dissolved in a cellulose nanofiber-based nematic LC. The bio-compatible LC ensures the excellent dispersity of the plasmonic-DNA nanostructures. Not only did this composite maintained the characteristic optical birefringence of LC materials, but it also featured photo-switchable CD due to the reconfigurable plasmonic-DNA nanostructures (Fig. 7) [103].

 

Fig. 7. Dissolving photo-switchable colloidal plasmonic DNA-origami in liquid crystals. Reproduced with permission from Ref. [103]. Copyright (2019) Optical Society of America.

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3. Applications of nanophotonic devices fabricated by DNA origami

3.1 Optic waveguides and antennas

With the help of DNA nanotechnology, unique photonic nano-patterns possessing molecularly engineered structures had been built from bottom-up that may find applications to tailor light-matter interactions that may serve as optic waveguides or antennas [104].

The ability of deterministically placing nanoparticles at nanometer precision makes DNA origami an ideal tool to set up desired plasmonic coupling among a collective of metal nanoparticles. Klein et al. fabricated a series of multi-scaffold DNA origami nanoparticle waveguides [105]. By tuning the docking sites on a rod-like DNA origami, the authors could control both the interparticle gap and their spatial arrangement. The as-prepared waveguides exhibited distinctive optical properties, which were in good agreement with theoretical calculations (Fig. 8(a)).

 

Fig. 8. Optical waveguides fabricated by DNA origami. (a) Chains of nanoparticles. Reproduced with permission from Ref. [105]. Copyright (2013) American Chemical Society. (b) Optical waveguides coupled to a fluorescent nanodiamond. Scale bars: 100 nm. Reproduced with permission from Ref. [106]. Copyright (2018) American Chemical Society. (c) Investigations on coupling efficiency on a hybrid three particle system. Scale bar: 100 nm. Reproduced with permission from Ref. [107]. Copyright (2017) Springer Nature.

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Gür et al. have further connected the waveguide to a fluorescent nanodiamond to investigate the nanoscale light propagation [106]. The ideal optic waveguide consisted of equally spaced, linearly arranged AuNPs, with gap size a couple of nanometers (Fig. 8(b)). The optical energy that input from one end of the waveguide could be transferred to the other end with low loss. The efficiency of energy transfer was related to the matching degree between the wavelength of the incident light and that of the plasmonic mode of the waveguide. For the 42 nm diameter AuNPs employed in the study, a longer incident wavelength (e.g. 600 nm) was better than a shorter one (e.g. 550 nm). However, when one of the AuNPs was removed from the waveguide, the energy transfer efficiency dropped dramatically. Further investigations revealed that a strong plasmonic coupling within nanoparticle waveguides could be achieved using a triple-particle unit, consisting of two AuNPs and a AgNP island in between [107], which displayed almost no dissipation of energy (Fig. 8(c)). The formation of strong hotspots among all particles was identified as the main mechanism for the lossless coupling and thus coherent ultrafast energy transfer between the remote partners.

By definition, an optical antenna is a device that efficiently couples the energy of free-space radiation to a confined region [104]. Such devices can be readily achieved by assembling plasmonic nanoparticles with DNA origami, as demonstrated in section 2.1. The most frequently used nanoantennas are AuNP dimers, which confines optical energy within their gap. By deterministically setting up the spatial relationship between the light source and the plasmonic system, DNA origami is capable of manipulating light-matter coupling [108,109]. For instance, it is possible to place a single emitter within a very small hot spot (e.g. 5 nm) of a nano-antenna to achieve high Purcell factors and emission enhancement [110]. A 5000-fold fluorescence enhancement was obtained using AuNP dimers that were placed on both sides of a DNA origami rod as the antenna (Fig. 9(a)). Directional emission from DNA origami-enabled nano-antennas may be achieved by tuning the relative angle between the polarization of the light and the geometric axis of the nanostructure. Hübner et al. showed that the far field single molecule emission pattern located in a DNA origami-assembled AuNP dimer could be switched between circular and dipolar modes via tuning the incident polarization [46]. This was due to the distinctive plasmonic modes of AuNP dimers along different directions.

 

Fig. 9. DNA origami assembled nanoantenna. (a) A nanoantenna with significantly enhanced emission efficiency. Reproduced with permission from Ref. [110]. Copyright (2015) American Chemical Society. (b) A nanoantenna for light harvesting. Reproduced with permission from Ref. [111]. Copyright (2016) American Chemical Society.

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DNA origami also enables rational design of light harvesting antenna structures [111]. The light harvesting efficiency of photoactive molecules that is highly dependent on their nanoscale architectures was studied with base-pair accuracy and full geometric freedom on the DNA origami platform (Fig. 9(b)). The antenna effect was found to increase linearly with the donor-to-acceptor ratio and inversely proportional to the average distance between the donor and acceptor, demonstrating DNA origami as a highly versatile tool for testing design concepts in artificial light-harvesting networks.

3.2 Manipulate energy transfer

The photonic nanostructures assembled by DNA origami possess excellent ability to control and tailor energy transfer and harvesting. A classic example is manipulating the quantum efficiency of fluorescent emitters by plasmonic nanoparticles. Known as nanometal surface energy transfer (NSET), the lifetime of an oscillating dipole could be greatly reduced when it was located at a short distance from a metal surface [112].

In our previous work, we placed a quantum dot (QD) and an AuNP on a triangular DNA origami. Their relative distance was tuned by programming the position of docking strands on the origami (Fig. 10(a)) [113]. Obvious decrease in the emission intensity of the QD was observed when it was within ∼55 nm of the AuNP. In addition, the emission lifetime was significantly reduced, indicating that the photonic energy absorbed by the emitter was lost quickly through non-emissive pathways. By carrying out a series of spectral characterizations, we discovered that the energy transfer is inversely proportional to the 2.7th power of the distance between nanoparticles with a half quenching distance at ∼28 nm.

 

Fig. 10. Quantum efficiency of a single emitter mediated by DNA origami. (a) A long range spectroscopic ruler. Scale bar: 100 nm. Reproduced with permission from Ref. [113]. Copyright (2014) American Chemical Society. (b) Gold nanostars. Scale bar: 50 nm. Reproduced with permission from Ref. [114]. Copyright (2014) Springer Nature. (c) Quantum efficiency modification using AuNP dimers. Scale bars: 100 nm. Reproduced with permission from Ref. [115]. Copyright (2013) American Chemical Society.

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Schreiber et al. achieved hierarchical assembly of metal nanoparticles, quantum dots and organic dyes using DNA origami scaffolds [114]. They first attached metal nanoparticles or emitters onto a 24-helix bundle, then assembled multiple of the bundles and nanoparticles to form complex clusters (Fig. 10(b)). Using this assembly method, the authors investigated the fluorescence quenching of organic dyes next to a single metal particle. It was found that the emission intensity got obviously reduced until the dye reached as far as ∼58 nm from the metal nanoparticle.

While a single metal particle showed clear NSET, an emitter placed between two plasmonic particles may experience more complicated situations. Besides NSET, the apparent emission intensity is also determined by an enhancement factor, which comes from the enhanced local electric field at the hot spot of the plasmonic nanostructures [52]. Consequently, the detected emission exhibit a dependence on the gap size of the nanoparticle dimer (Fig. 10(c)) [115]. Enhanced emission was recorded at small gap sizes (e.g. 20 nm), while no enhancement was found at large gaps (e.g. 52 nm). In addition, the emission was also found to rely on the excitation light polarizations. Polarization that matched the longitudinal plasmonic mode of nanoparticles dimers resulted in much stronger fluorescent signals.

Energy transfer between multiple dyes may also be assisted by DNA origami as spatial ruler. Anderson et al. placed an AuNP under an array of dyes with the help of DNA origami (Fig. 11(a)) [116]. When a pair of Förster resonance energy transfer (FRET) dyes simultaneously presented in the range of the localized surface plasmon resonances (LSPR) of the AuNP, the energy transfer between the dyes was enhanced. A better efficiency of enhancement was observed when the LSPR wavelength overlapped with the excitation and emission maximum of the dyes. This was attributed to plasmon resonance energy transfer, which is promising for the future design of biomimetic energy collection systems.

 

Fig. 11. Mediating the energy transfer between different dyes. (a) FRET mediated by the LSPR of AuNPs. Reproduced with permission from Ref. [116]. Copyright (2019) American Chemical Society. (b) An array of FRET dyes. Reproduced with permission from Ref. [117]. Copyright CC BY-NC 3.0.

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Without plasmonic nanoparticles, DNA origami platform alone was also able to improve FRET efficiency. This was achieved by organizing coupled dyes into an array, in which the relative position of each component was accurately defined [111,117]. By changing the number and arrangement of different fluorophores, the light harvesting efficiency was optimized to create a broadband absorption and the energy transfer to the acceptor was boosted by several times (Fig. 11(b)).

3.3 Surfaced enhanced Raman scattering

Surfaced enhanced Raman scattering (SERS) offers orders of magnitude increases in Raman intensity when the molecule is located on or close to a rough metal surface [118]. Although many factors have been proven to contribute to the enhancement of Raman scattering, the dominant contributor is believed to be the increased local electric field (E-field) [118,119]. Molecules locating in an enhanced E-field emit much stronger Raman signals, which improves the sensitivity of spectral analysis.

Significantly boosted E-field has been observed in a number of plasmonic nanostructures [120,121]. It is found that the strongest E-field usually appeared at the tips, gaps or cavities of nano-features, which are commonly known as hot spots. Therefore, constructing those geometric units in a controllable manner is highly desirable in SERS measurements. With the great patterning ability, DNA origami is a good choice to fulfil this mission. In early examples, plasmonic hot spots were created by assembling two AuNPs on the same edge of a triangular DNA origami [122]. A more popular design is employing AuNP dimers separated by a DNA origami [123], in which a very strong E-field presents at the gap between the nanoparticles. SYBR Gold, a minor groove-binding fluorescent nucleic acid stain were used to test the system. This molecule has a high affinity to double-stranded DNA (dsDNA) and may evenly distribute in the origami after incubation. Enhanced characteristic Raman bands of SYBR Gold was observed, whose intensity showed a dependence on incident polarization (Fig. 12(a)). This design possesses extraordinary ability to align the analyte and the hot spot with nanometer accuracy, however, the hot spot is filled up by DNA origami. As a result, external molecules or large biomolecules may be difficult to enter the plasmonic gap, except those DNA binding dyes.

 

Fig. 12. SERS platforms based on spherical AuNPs. (a) An AuNP dimer separated by a planar DNA origami. Reproduced with permission from Ref. [123]. Copyright (2014) American Chemical Society. (b) AuNR dimers mounted on a DNA origami rack. Reproduced with permission from Ref. [124]. Copyright CC BY 4.0. (c) DNA origami-templated metamolecules. Reproduced with permission from Ref. [125]. Copyright (2020) American Chemical Society.

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Thacker et al. applied a different strategy to assemble the AuNP dimers [124]. Two spherical particles were mounted onto a DNA origami rack, on the sides of a middle ridge, while the inter-particle gap was maintained at about 3.3 nm (Fig. 12(b)). The hot spot between the AuNPs was kept as a void space that allowed external analytes to diffuse into. Using Rhodamine 6G as a model molecule, the enhancement factor of SERS was measured to be 10⁵-10⁷. It is possible to use this setup to distinguish different DNA sequences.

Besides metal particle dimers, DNA origami-templated metamolecules composed of multiple metal nanospheres was also employed in SERS applications [125,126]. Ag@Au core-shell nanoparticles were firstly grown into hexagonal units via DNA origami templated assembly. This unit could be further assembled into larger clusters (Fig. 12(c)). As the structure grew larger, the Raman enhancement factor increased, which was proportional to the magnitude of the local E-field.

Metallic bowtie nanoarchitecture can produce dramatic E-field enhancement, which is advantageous in single molecule analysis and optical information processing [127]. Such structures were usually fabricated by top-down methods such as EBL and PL [127,128], but a small gap at the center of the bowtie was hard to achieve. Taking advantage of DNA technology, Zhan et al. accurately assembled nano-bowties on a DNA origami board [129]. The average gap size was about 5 nm. When a single analyte molecule was anchored within the gap, decent Raman signals could be recorded (Fig. 13(a)). The SERS enhancement factor in the experiments was evaluated to reach ∼10⁹.

 

Fig. 13. Other designs of SERS substrate assembled on DNA origami. (a) Nano-bowties. Reproduced with permission from Ref. [129]. Copyright (2017) Wiley-VCH. (b) Gold nanostars. Reproduced with permission from Ref. [130]. Copyright (2017) American Chemical Society.

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Gold nanostars rich in sharp tips can also be excellent structure to achieve strong local E-field. Dimers of gold nanostars were assembled on a DNA origami board (Fig. 13(b)). The SERS enhancement factors of single Texas Red dye molecules located in the conjunction region with interparticle gaps of 7 and 13 nm reached 2 × 10¹⁰ and 8 × 10⁹, respectively [130].

3.4 Sensors

The ability to sense external or internal stimuli is critical to living creatures. As of today, a variety of sensors have been developed to detect environmental changes, diseases and potential harmful materials based on DNA origami [131–133]. The reliable programmability of DNA origami makes it an extremely attractive tool for prototyping novel sensing systems, especially photonic sensors. In general, previously developed DNA origami-based sensors could be classified into two groups depending on the type of target species. Some of the devices are sensitive to regular stimuli such as pH, heat and voltage, while the others response to specific molecular targets, e.g. aptamer and antibodies [134,135]. The sensing mechanism generally depends on stimuli-mediated reconfiguration of DNA origami structures.

A temperature sensor based on DNA nanostructures can be readily made depending on the intrinsic heat responsive nature of DNA. When heated to a sequence-dependent melting temperature, dsDNA will dissociate, leading to deformation of the original structure [136]. A DNA assembled chiral plasmonic system was applied for temperature detection [137]. The initial angle between two AuNRs was defined by a couple of tethers on DNA origami. As temperature rose, the tethers broke up and the angle between the AuNRs rotated, resulting in changes in CD (Fig. 14(a)). By programming the tether strands (sequence and length), it is possible to tune the response temperature of the sensor.

 

Fig. 14. DNA origami-based sensors. (a) A temperature sensor based on CD. Reproduced with permission from Ref. [137]. Copyright (2018) American Chemical Society. (b) Optical voltage sensing using DNA origami. Reproduced with permission from Ref. [140]. Copyright (2018) American Chemical Society.

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A DNA-based pH sensor is also relatively easy to design, as quite a few DNA structures are known to be pH responsive. I-motif, for example, forms two distinctive structures under low and high pHs [138,139], which is an ideal candidate to realize the pH-sensitive function.

It is also possible to trigger conformational change of DNA origami by applying an external voltage. The voltage sensing mechanism can be intuitively understood as a rope pulling on the DNA origami plate. Since DNA is negatively charged in the buffer, the pulling force directly depends on the strength of the electric field applied. Accordingly, optical-voltage sensing using DNA origami has been realized [140]. The voltage change controlled the distance between a single pair of FRET dyes. When the voltage was on, the donor was pulled away from the acceptor, leading to brighter green color and weakened red emission (Fig. 14(b)).

Taking advantage of the specific binding between DNA and the target analytes, a large variety of sensing systems have been developed. Chiral plasmonics have been extensively applied for DNA, RNA and aptamer detections [137,141,142]. External DNA or RNA strands that were complementary to the lock strands extending on DNA origami could form double-strand tethers, which were able to rotate part of the origami structure (Fig. 15(a)). As a result, the AuNRs attached to the DNA origami would spin accordingly, leading to variations in CD response. Depending on the design of lock strands, the chirality could either be turned on and off, or the handedness could be completely switched during the detection.

 

Fig. 15. DNA origami-based sensors for specific target molecules. (a) An aptamer sensor based on CD response. Reproduced with permission from Ref. [141]. Copyright (2018) American Chemical Society. (b) An antibody sensor. Reproduced with permission from Ref. [145]. Copyright CC BY 4.0. (c) A FRET based aptamer sensor. Reproduced with permission from Ref. [146]. Copyright (2017) American Chemical Society.

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Fluorescent sensors have also been devised to detect specific targets [143]. Some antibodies, for example, strongly bind with dsDNA and break some of the base pairing interactions [144]. Based on this, a turn-off fluorescent sensor that responded to an autoimmune antibody ED-10 was fabricated [145]. The DNA origami was initially saturated with a fluorescent intercalating dye. The binding of the autoimmune antibody reduced the number of dye molecules that were bound to DNA and changed the micro-chemical environment, leading to reduced fluorescent emissions (Fig. 15(b)).

Walter et al. developed an aptamer sensor based on FRET dyes [146]. Without the analyte, the DNA origami showed an open structure, in which the FRET dyes were well separated. Only green emission from the donor dye was detected. Under the presence of aptamers, the origami was closed, leading to a close contact between the donor and acceptor. Consequently, red emission from the acceptor started to be observed (Fig. 15(c)).

4. Conclusions and perspective

As a bottom-up fabrication technique, DNA origami assisted self-assembly possesses extraordinary patterning ability. DNA origami templates can be shaped into almost any arbitrary shapes and architectures that can direct the formation of designed nanostructures. Modern organic chemistry enables a series of functional modifications on DNA sequences, which allows DNA origami to specifically interact with other material systems, including but not limited to metallic nanoparticles, semiconductor nanoparticles and organic fluorescent emitters. The fixed geometry of dsDNA, as well as the strict paring rule make the structure of the designed DNA origami highly predicable, and it is possible to organize different structural units in a functional system with nanometer accuracy.

Taking these advantages, DNA origami has been widely employed in bottom-up assembly of a large variety of photonic nanomaterials. Well-controlled nanostructures, from nanocavities, chiral structures to 2D and 3D clusters and arrays have been designed and constructed via DNA origami assisted self-assembly. Many fundamental studies were made possible to understand and control light-matter interactions using DNA origami as a nano-meter scale pegboard and 3D scaffold. Many of the as-obtained products exhibited distinct optical properties and could find promising applications in optical devices, SERS detection, regulating energy transfer and sensors. Due to page limit, not all important applications were discussed. DNA-PAINT technique, for example, has been utilized in super resolution microscopy and greatly boosted the resolution [147].

In addition to the already developed fields, some potential directions that may benefit from involving DNA origami are note-worthy.

Utilizing the great patterning capability of DNA origami to fabricate complex yet useful photonic structures that are challenging for other approaches is of tremendous significance. Yagi-Uda antenna, for example, is widely known for its highly directional emission [148]. Although nano-sized Yagi-Uda antenna has already been fabricated, the quality of the feature is far from satisfactory [149]. Being able to construct such systems with DNA origami will greatly facilitate the development of nanophotonics.

Another promising direction is biomimetic optical systems. The light harvesting ability of plants has been served as the foundation of our food chain for millions of years. The key to photosynthesis is high efficiency of light harvesting and energy transfer enabled by the exquisite organization of light absorbing pigments in the complex assembly of photosynthesis systems and many synchronized cycles of enzyme-catalyzed reactions [150]. To create efficient artificial energy harvesting machines to mimic photosynthesis, it is desired that DNA origami nanopatterning technologies can be applied to integrate and couple functional units with molecular precision.

With the advance of DNA nanotechnology, more reliable ways have been developed to construct DNA origami with high yield, high accuracy, dynamic behaviors, larger assembly with lower cost, DNA origami templated assembly were made more feasible and more robust, a booming progress in this field in the future is expected, not only in the direction of nanophotonic applications, but also in the wider development of biophysical and biomedical applications, potentially in disease detection/prevention/therapeutics, photodynamic therapy, genetic engineering, immunotherapy, etc. There are many more to be explored.