DNA Nanostructure-Guided Plasmon Coupling Architectures

Abstract

Open AccessCCS ChemistryMINI REVIEWS15 Nov 2022DNA Nanostructure-Guided Plasmon Coupling Architectures Mengmeng Liu, Xiaoyu Zhang, Lulu Huang, Jie Li, Chunhai Fan and Yang Tian Mengmeng Liu Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 Google Scholar More articles by this author , Xiaoyu Zhang Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 Google Scholar More articles by this author , Lulu Huang Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 Google Scholar More articles by this author , Jie Li Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 Google Scholar More articles by this author , Chunhai Fan School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240 Google Scholar More articles by this author and Yang Tian *Corresponding author: E-mail Address: [email protected] Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241 Google Scholar More articles by this author https://doi.org/10.31635/ccschem.022.202202387 SectionsAboutAbstractPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareFacebookTwitterLinked InEmail Plasmon coupling architectures with specific spatial and orientational arrangement configurations possess unique and tailored plasmonic properties and hold promise for advancements in nano-optics, nanoantennas, and biosensors. Numerous research has focused on the construction of plasmonic assemblies with predetermined configurations. DNA nanostructures with arbitrary geometry, high compatibility with metal nanoparticles, and spatial addressability meet the requirement for precise spatial and orientation arrangement. Currently, DNA nanostructures are widely exploited as structural materials to generate plasmonic structures with well-defined topologies. We review the evolution of DNA nanostructure-guided plasmon coupling architectures, including the introduction of DNA nanostructures, DNA modification on the surface of plasmonic nanoparticles, and three strategies for constructing complex plasmonic nanostructures. Then we focus on the emerging applications of DNA nanostructure-guided architectures with engineered local electromagnetic enhancement for modulating plasmon coupling, amplifying emitter signals, and serving as biosensors. Finally, we will critically discuss the challenges and opportunities in this field. Download figure Download PowerPoint Introduction Localized surface plasmon resonance (LSPR), a long-studied nanoscale optical phenomenon, is produced when incident light excites conduction electrons at the surfaces of noble metal nanoparticles.1–4 It produces strong electromagnetic enhancements as well as sharp absorption and scattering peaks. The intensity and frequency of the LSPR peak are highly dependent on the shape, size, chemical composition, and surrounding environment of the nanoparticles.5–9 In particular, when nanoparticles are positioned close together to create advanced plasmonic nanostructures, the plasmon of neighboring nanoparticles hybridizes, resulting in plasmon coupling.10–13 According to the theory of plasmon hybridization,14 the characteristics of plasmon coupling are determined by the material composition, nanoparticle size, and spatial and orientational configuration of neighboring nanoparticles. Thus, the near-field plasmon coupling between nanoparticles is diverse and tunable, enabling nanostructures to easily access explicitly tailored optical properties and optical phenomena (such as plasma hybridization, Fano resonance, chiral response, etc.).15,16 For instance, the relative positioning of assembled nanoparticles can be manipulated to tailor the electromagnetic enhancement of architecture.17,18 Thus, to realize their application in biosensors,19 imaging20,21 metamaterials,22,23 and nanoantennas,24–26 nanoparticles have to be meticulously organized in plasmon coupling architectures. To fabricate plasmon coupling architectures with predefined configurations, researchers have described a series of physical (optical, electrical, or mechanical interactions) and chemical (small molecule, polymer, or biomacromolecule) approaches.27–29 Among them, high-rigidity DNA nanotechnology satisfies the requirement for precise arrangement.15,30 DNA nanostructures are programmed using Watson–Crick base-paring and can be functionalized with a variety of molecules or nanoparticles that have defined numbers and positions.31–33 DNA nanostructures possess great potential in the fabrication of plasmon coupling architectures compared with other traditional materials.34 First, DNA nanostructures with arbitrary two-dimensional (2D) and three-dimensional (3D) geometries, which could serve as templates for arranging nanoparticles, provide the possibility for the construction of complex plasmonic nanostructures.35 Second, DNA nanostructures attach to metal nanoparticles through facile covalent or noncovalent surface modification, allowing the formation of highly stable and valence-controllable metal nanoparticle conjugations.36,37 Third, the sequence-specificity and spatial addressability of DNA nanostructures provide a novel method for placing metal nanoparticles with defined numbers and positions.38,39 To date, there are outstanding reviews that have systematically summarized the plasmon coupling architectures.35,40,41 The majority of them are primarily centered on the techniques that align metal nanoparticles by directly placing them on DNA nanostructures. The indirect techniques, including DNA printing and DNA-templated metallization, have not been thoroughly discussed. Meanwhile, the various applications of plasmon coupling architectures, such as nano-optics, nanoantennas, and biosensors, have not been comprehensively summarized. In this review, we aim to summarize the significant advances in the construction of DNA nanostructure-guided plasmon coupling architectures. We will first describe the development of DNA nanotechnology, the methods for creating DNA-metal nanoparticles conjugations, and DNA nanotechnology-guided assembly techniques for plasmon coupling architectures with specified spatial and directional configurations. Subsequently, we discuss how plasmon coupling architectures can be used to modulate plasmon coupling, amplify emitter signals, and serve as biosensors. Finally, we will discuss the remaining obstacles and perspectives on future directions in this field. Construction of Plasmon Coupling Architectures via DNA Nanostructures DNA nanostructures DNA nanotechnology has been widely used to create nanoscale architectures using a “bottom-up” approach due to their unique structural motifs and self-recognition capabilities.42 In the 1980s, motivated by the Holliday junction used for genetic information exchange, Seeman43 presented the configuration of immobile junctions. These junctions were connected directly to form a double-crossover molecule (DX) in which they behaved as “valence clusters” of macromolecules. This work marked the beginnings of the tile strategy, which permitted the massive parallel creation of well-defined 2D and 3D DNA nanostructures. Then, to expand the geometry of DNA nanostructures, Fu and Seeman44 created various rigid tiles that can be used to fabricate high-order periodic DNA assemblies, such as lattices and 3D nanostructures. In addition to junctions, He et al.45 created star-shaped motifs as construction blocks. By manipulating the flexibility and concentration of motifs, DNA buckyballs, DNA tetrahedra, and DNA dodecahedra were constructed using motifs with specific point numbers and angles. Wei et al.46 reported a universal assembly methodology using single-stranded tiles (SST) as DNA bricks. With the SST bricks, larger structures were created, including solid shapes with complex geometries and surface patterns and hollow shapes with intricate tunnels and enclosed cavities.47 Compared with conventional tile-based assembly methodologies, this strategy is more customizable in terms of geometry and more fault tolerant. DNA origami is another effective method for fabricating DNA nanostructures with subnanometer accuracy and high yield in the range of 50–500 nm. Rothemund48 first proposed the concept of DNA origami in 2006. In this work, a long single ssDNA (scaffold), typically M13mp18, greater than 7000 nucleotides, was folded into a predesigned shape using 200–250 short ssDNAs (staples). This technique produced asymmetric shapes like the dolphin shape49 and the China map,50 as well as symmetric shapes like squares, triangles, and five-pointed stars.48 To obtain 3D DNA origami, Douglas et al.51 then developed a honeycomb lattice by fabricating pleated layers and applied it to fold into 3D nanostructures such as the monolith, square nut, railed bridge, genie bottle, stacked cross, and slotted cross. Zhang et al.52 and Andersen et al.53 proposed an additional 3D nanostructure construction technique. They utilized the 2D origami sheets as faces and constructed DNA boxes and hollow 3D tetrahedron cages. Han et al.54 developed a method for constructing self-assembling DNA nanostructures with defined, intricately curved surfaces to regulate the curvature of 3D DNA nanostructures. Specifically, they produced in-plane curvature by bending helical DNA and introduced out-of-plane curvature by fiddling with crossover networks in DNA origami. Using this method, 3D spherical shells, ellipsoidal shells, and nanoflasks with complicated curved surfaces were fabricated. In this collection, DNA origami was made from staples with specific sequences and positions. This means that the DNA nanostructures can be used as a framework or pegboard to attach functional molecules or nanoparticles in specific places. To build larger-sized DNA hierarchical superstructures, origami and DNA tiles have been used as programmable modules. Zhao et al.55 utilized DNA origami or tile instead of short ssDNA as a staple for folding the scaffold into prefabricated 2D-array patterns. Using local assembly rules, Tikhmoirov et al.56 developed the “fractal assembly” and created sophisticated DNA-origami arrays that could be applied to render irregular images. Three-dimensional DNA frameworks with larger sizes, such as icosahedrons and polyhedrons, were also constructed using origami bundles and tripod tiles.57 Yao et al.58 applied submicrometer helix bundles as building blocks for a variety of intricate structures, including multiarm junctions, polyhedrons, and lattices. Due to their addressing properties, hierarchical superstructures offer a method for integrating specific DNA-metal hybrid nanostructures, similar to DNA origami. Dynamic DNA nanostructures have also been created, in addition to intricate static structures. Because of their remarkable ability to respond to specific stimuli, dynamic nanostructures have been designed to perform specific and computational tasks on demand.59 Typically, DNA hybridization and dehybridization, ion concentration, and pH stimulation are the fundamental strategies for achieving dynamic structural reconfigurations. Song et al.60 reported the construction of reconfigurable DNA structures using origami and single-strand-brick techniques. By altering their internal shape through DNA trigger strands, the arrays were able to transmit long-distance, predetermined data. Recently, Zhang et al.61 demonstrated a pH-activated, shape-resolved nanomechanical device based on DNA nanocalipers. Conjugation of DNA and metal nanoparticles Chemically tagged DNA, such as thiol- and selenol-modified DNA, and DNA with high base affinities, such as polyA, are facile to conjugate with metal clusters or metal nanoparticles, thereby supporting sequence-specific recognition for nanoparticle assembly.62–64 Since the report in 1996 of the formation of DNA-gold nanoparticle (AuNP) conjugations by Mirkin et al.65 and Alivisatos et al.,66 these DNA–AuNP conjugations have promoted the development of DNA nanostructure-guided metal architecture self-assembly, which has led to tremendous advances in physics, chemistry, and biology.42 Covalent linking The thiol anchor group is widely applied to conjugate DNA on the surfaces of metal nanoparticles. The formation of a covalent Au–S bond is a straightforward chemical reaction between the surfaces of metal nanoparticles and the thiol groups of biomolecules such as DNA. Meanwhile, the Au–S bond remains stable despite varying conditions. Mirkin et al.65 and Alivisatos et al.66 demonstrated that thiol-modified oligonucleotides can be attached to AuNPs. Demers et al.67 reported a “salt-aging” method for attaching thiol-modified-ssDNA onto the surface of AuNPs (Figure 1a). Typically, AuNPs and thiol-modified ssDNA were mixed at a predetermined ratio, and then NaCl was added slowly until the final concentration reached 1.0 M (0.05 M increase). The salting process was followed by an overnight incubation at room temperature. In this method, the size of the AuNP is crucial for determining the ratio of AuNPs to ssDNA and the length of ssDNA. In particular, for larger particles, a higher number of ssDNA strands or longer ssDNA strands are required to stabilize DNA–AuNP conjugations. Hurst et al.68 discovered that the DNA loading increases by two orders of magnitude as the gold nanoparticle size increases from 15 to 250 nm. Liu et al.69 applied a large amount of ssDNA to produce monodispersed DNA–AuNP conjugations (50 nm in diameter) that were stable outside the cell. Figure 1 | Scheme for construction of DNA-gold conjugations via covalent bonds. (a) Salt-aging modification method for formation Au–S bonds. Adapted with permission from ref 67. Copyright 2000 American Chemical Society. (b) pH-assisted modification method for formation of Au–S bonds. Adapted with permission from ref 70. Copyright 2012 American Chemical Society. (c) Freeze–thaw method for formation Au–S bonds. Adapted with permission from ref 71. Copyright 2018 American Chemical Society. (d) Preparation of dithiol-modified ssDNA and dithiol-modified AuNP–DNA conjugates. Adapted with permission from ref 74. Copyright 2008 American Chemical Society. (e) Preparation of SeH-modified DNA molecular beacon, and the detection mechanism and anti-interference preformation of Se-modified AuNP–DNA conjugates. Adapted with permission from ref 76. Copyright 2020 American Chemical Society. Download figure Download PowerPoint Typically, the “salt-aging” method requires more than 40 h to modify the DNA on the surface of AuNPs. To accelerate the modification reaction rate, Zhang et al.70 suggested a pH-assisted DNA modification approach, where the surface charge density was reduced by lower pH, and then thiol-modified DNA was rapidly adsorbed on the surface of AuNPs (Figure 1b). Using the pH-assisted modification approach, it was completed in a matter of minutes. Moreover, the pH-assisted modification approach enabled the quantitative adsorption of DNA, removed the procedure to count the number of adsorbed DNA, and reduced the procedure to remove the free ssDNA strands. As a result, this method permitted the adsorption of multiple DNAs with distinct sequences in predetermined ratios. To maximize the DNA loading on the surface of nanoparticles, Liu et al.71 reported a freeze–thaw technique without the use of any extra chemicals or reagents (Figure 1c). Like the pH-assisted DNA modification approach, the freeze–thaw approach completed DNA modification in a few minutes. Moreover, this approach was advantageous for producing AuNP-based nanoflares since DNA hybridization could be promoted at lower temperatures. Utilizing the unique physical process that occurs when water freezes, the freeze–thaw method could be applied to a variety of biological or nanosystems. New anchor groups are required to improve the stability of DNA–AuNP conjugations in the biological environment, specifically to prevent the displacement of ssDNA from AuNPs by abundant biothiols. Thiol-based anchoring groups,72–74 such as steroid cyclic disulfide and trithiol, were developed for linking oligonucleotides to metal nanoparticles in aqueous conditions (Figure 1d). Compared with traditional gold conjugates with monothiol linkers, the multithiol anchors are more resistant to thiol attacks (such as glutathione), which have a negative impact on subsequent hybridization reactions. Li et al.73 applied trithiol-capped oligonucleotides to modify AuNPs with a diameter of 30 nm. The construction of the Au–Se bond is another strategy for enhancing the stability of DNA–AuNP conjugations. DNA–AuNP conjugation with an Au–Se bond is more resistant to complex biological microenvironments due to the significantly higher bond energy of Au–Se compared with Au–S.75 Gao et al.76 and Liu et al.77 synthesized a selenol-terminal functionalized molecular beacon (MBSeH), which was subsequently used to prepare a Au–Se bond-based DNA–AuNPs conjugation (Figure 1e). In this work, the Au–Se bond prevented interference from biological thiols and eliminated detection distortions during live cell biomarker imaging. In addition to AuNPs, AgNPs are extensively utilized in the fabrication of plasmonic architectures. Despite the considerably weaker Ag–S bond, thiol-modified DNA can still be used to modify silver nanoparticles. Compared with AuNPs, the salt-aging approach for DNA–AgNPs conjugations requires a much slower salt-adding process and more time for modification. Zhang et al.78 discovered that it was also possible to modify AgNPs with the aid of pH-assisted technology, and the process is quick. Lee et al.79 also discovered that cyclic disulfide anchoring groups could be used to increase the stability of DNA–AgNP conjugations. Noncovalent linking For nanoparticle hybridization, it is essential to adjust the valence and conformation of oligonucleotides on the surface of nanoparticles. However, the valence-controlled DNA–AuNPs conjugation is typically unstable in salty solutions and low yielding. To improve the precise control of the valence and conformation of oligonucleotides, deblock polyadenine (polyA)-oligonucleotides are applied to the associated metal surface due to the higher relative affinity of adenine nucleobase for gold than other nucleobases. Pei et al.80 proposed a novel polyA-DNA functionalization method. In this work, polyA was employed as an efficient anchoring block for preferential interaction with the surface of AuNP, and the recognition block in ssDNA strands assumed an upright conformation that was helpful for DNA hybridization (Figure 2a). Changing the length of the polyA block can modulate the valence of DNA on the surface of AuNPs. Typically, the density of DNA falls as the length of the polyA block increases.81 Following that, Yao et al.82 applied ssDNA with an 80-block polyA to produce monovalent DNA–AuNP conjugations with a nearly quantitative yield of 90%. Then, Chen et al.83 modulated the configuration of monovalent DNA–AuNP conjugations by programming the DNA bond energy and bond length. Using DNA encoders with different arrangements of polyA and binding domains, three types of DNA motifs with different topologic configurations were assembled (Figure 2b). Yao et al.84 also modulated the valence state of DNA by programming the arrangement, length, and sequence of DNA encoding regions containing polyA and binding domains (Figure 2c). Figure 2 | Scheme for construction of DNA-gold conjugations via noncovalent bonds. (a) Deblock oligonucleotides and formation of DNA-gold conjugations. Adapted with permission from ref 80. Copyright 2012 American Chemical Society. (b) Concept and design of monovalent DNA–AuNP conjugations in three different types (I–III). Adapted with permission from ref 83. Copyright 2020 Springer Nature. (c) Concept and design of DNA–AuNP conjugations with different valence state. Adapted with permission from ref 84. Copyright 2020 Springer Nature. Download figure Download PowerPoint Similar to their sulfurized counterparts, Zhang et al.85 attached polyA–DNA to the surface of AuNPs and achieved high DNA loading capacity by pH-assist techniques. Then, Hu et al.86 published a freezing technique for creating polyA-based DNA–AuNPs conjugations. They demonstrated that 10 A bases at the sequence ends were necessary for labeling stability and that increasing the polyA-base number was a practical method for overcoming unsuccessful or ineffective labeling. Huang et al.87 then published a novel microwave-assisted heating and drying approach to modify nonthiol-tagged DNA on the surface of AuNPs, in which a standard microwave oven was employed to rapidly evaporate water. The heating–drying method accomplished DNA modification in a matter of minutes. This technique produced DNA–AuNP conjugate with excellent sequence versatility and highly stability. Additionally, they demonstrated that, unlike conventional approaches, the microwave-assisted dry heating method could attach long-chain nucleic acids, such as CRISPR/Cas9-sgRNA, to the surface of AuNPs. Selective modification for anisotropic nanoparticles The positioning of DNA on the surface of anisotropic nanoparticles is regulated by selective modification techniques, which are frequently used to modulate the orientation of anisotropic nanoparticles. Anisotropic structures, such as nanorods and nanoprisms, have distinct crystal properties at their tips and sides, which have distinct binding propensities for thiol-modified ssDNA. This discovery makes it possible to selectively modify anisotropic forms at specific locations. Xu et al.88 published a method for the selective DNA oligomer modification of nanorods. Because hexadecyl trimethyl ammonium bromide (CTAB) prefers the side faces of Nanorods (NRs),89 the terminals of NRs are more susceptible to thiol-modified DNA-oligomers attachment. In this study, different oligonucleotides with low and high concentrations were used in two modification steps, enabling tip-specific, side-specific, and nonspecific modifications (Figure 3a). Coughlin et al.90 also reported a light-mediated approach for physically positioning different DNA strands in the designated areas of gold nanostars. In this work, a fs-laser pulse was used to release strands from the terminals of nanostar branches that had already been modified with one ssDNA strand. Then the empty spaces on the gold nanostars were modified by a second strand (Figure 3b). These techniques for selective modification are often employed to manage complex nanoscale assemblies91 and tip-specific fluorescence enhancement.92 Figure 3 | Selective modification for anisotropic nanoparticles. (a) Schematics of selective modification of nanorods by adjusting the concentration of different oligonucleotides. Adapted with permission from ref 88. Copyright 2012 American Chemical Society. (b) Schematics of selective modification of nanostars by a light-mediate approach. Adapted with permission from ref 90. Copyright 2021 American Chemical Society. Download figure Download PowerPoint Fabrication strategies of DNA nanostructure-guided plasmon coupling architectures DNA strands have been extensively used to connect nanoparticles to construct assemblies. Under the guidance of DNA, Hao et al.29 assembled strong plasmon coupling nanodimers with a 1.25 nm gap using a solvent-driven process. With the emergence of DNA nanotechnology, nanostructure-based methods have been developed to meet the fabrication requirements of positioning nanoparticles precisely and quantitatively in three-dimensional space. Due to their high rigidities, high assembly yields, and inherent sequence-defined addressability,93 DNA nanostructures are ideal for producing massive AuNP nanostructures with distinctive structural complexity and adaptable optical characteristics. Alignment of metal nanoparticles by direct placement; “overgrowth” of small metal NPs (typically AuNP, AuNR, and AgNP) by DNA-templated metallization; and transfer of discrete DNA spatial patterns to plasmon coupling architectures by printing are the three primary strategies for creating DNA nanostructure-guided plasmonic nanostructures. Alignment of metal nanoparticles by direct placement Generally, metal particles modified with one or more DNA linkers can be assembled at predefined binding sites of DNA nanostructures via hybridization with the corresponding DNA strands that are stretched from the DNA nanostructures. Sharma et al.74 proposed a method to place 10 nm spherical AuNPs at exact positions and build discrete gold nanoparticle patterns. In this work, a small amount of dithiol-modified DNA was applied to create monofunctionalized DNA–AuNP conjugations, and many short oligonucleotides were used to stabilize the conjugations (Figure 4a). Then, the structure was folded into origami using an AuNP-modified staple strand rather than the ssDNA staple strand. Atomic force microscopy measurements revealed that the yield of metal-modified DNA origami reached 91%. Subsequently, Pal et al.94 utilized triangular origami to construct a AgNP architecture with a predetermined center-to-center distance and number (Figure 4b). Moreover, the thickness of the origami could be employed to regulate the spatial spacing between nanoparticles. Acuna et al.95 described a method for assembling AuNP dimers with a separating spacing of 23 nm using pillar origami. With a two-layered DNA origami sheet, the separation distance between AuNPs was reduced to 5 nm.96 Figure 4 | Schematics and TEM images for DNA nanostructure-guided plasmonic nanostructures. (a) Cartoons showing DNA nanostructures carrying one and two AuNPs. Adapted with permission from ref 74. Copyright 2008 American Chemical Society. (b) Illustration and TEM images of DNA nanostructure guided-AgNPs nanostructures (I–IV) with different center-to-center distances. Adapted with permission from ref 94. Copyright 2010 John Wiley & Sons. (c) Design principle and scanning electron microscopy (SEM) characterization of super-origami DNA-guided gold nanostructures with n-tuples. Adapted with permission from ref 98. Copyright 2019 AAAS. (d) Scheme for the preparation of stimulus-responsive AuNR assemblies on DNA nanostructures. Adapted with permission from ref 106. Copyright 2017 American Chemical Society. Download figure Download PowerPoint In addition to controlling particle spacing, DNA nanostructures enable the regulation of organization patterns of plasmonic nanoparticle. Ding et al.97 applied triangular origami to organize six nanoparticles of varying sizes into centrally symmetric chains with less than 10 nm distance between each one. Fang et al.98 revealed a universal method for precisely arranging massive AuNPs (50 and 80 nm in diameter) with super-origami DNA frameworks. They designed DNA super origami with n-tuple docking sites as templates for assembling big AuNPs, and then anchored the nanoparticles at the predesigned locations by DNA hybridization. The super origami with n-tuple docking sites enabled the formation of 2n distinct geometries of nanoassemblies of varying shapes by designing unique anchoring strands (Figure 4c). In addition, DNA nanostructures have organized a variety of plasmonic nanostructures with 3D, twisted, and curled geometries. By selective modification, DNA nanostructures were extensively used to control the orientation of nanorods, as orientation is a crucial factor in the arrangement of anisotropic nanoparticles.99,100 Pal et al.101 used triangular origami to regulate the orientation of nanoparticles and guide the self-assembly of plasmonic nanostructures with various inter-rod angles and distances. In this work, DNA–AuNR