DNA-Based Gold Nanoparticle Assemblies: History
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Contributor:
Mo Xie
,
Jinke Jiang
,
Jie Chao

Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are organized in a highly precise and controllable way under the mediation of DNA, achieving programmability and specificity unmatched by other ligands. The successful construction of abundant gold nanoparticle assembly structures has also given rise to the fabrication of a wide range of sensors, which has greatly contributed to the development of the sensing field. 

  • DNA strands
  • DNA nanostructures
  • gold nanoparticle

1. Gold Nanoparticle Multimers

The properties of gold nanostructures are related to their shape, size and spatial arrangement. Assembling gold nanoparticles with well-defined structures and quantities in a specific space enables the specific amplified modulation of electronic, magnetic and optical signals. Owing to the unique self-assembly ability of DNA, gold nanoparticles can be organized in a highly precise and controllable way by precisely designing DNA sequences or DNA nanostructures to obtain Au NP multimers with well-defined structures and functions.

1.1. DNA Strand-Mediated Assembly

Coupling thiol-modified DNA molecules onto the surfaces of Au NPs through Au-S bonds is a common approach to functionalizing Au NPs. Liang et al. designed and modified complementary single-strand DNA sequences on AuNPs with diameters of 200 nm and 40 nm, respectively. Then, core-satellite nanostructures were formed through base complementary pairing hybridization. Subsequently, further silicification yielded a stable nanocavity called the DNA-silicified template for a Raman optical beacon (DNA-STROBE) model [1]. This structure provides a universal method for ultrasensitive label-free sensing exploration. In addition to monothiol DNA modification and hybridization self-assembly strategies, the dithiol DNA strand cross-linking strategy can also achieve the organization of Au NPs. Liu et al. employed a dithiol adenosine triphosphate (ATP) aptamer as a cross-linking molecule and assembled a porous cross-linking structure of gold nanotriangles (AuNTs) at the tip of the capillary to construct a SERS-electrochemistry nanopore platform for ATP detection, which showed higher SERS activity than that of conventional gold nanoparticles [2].
However, in the above strategies, thiol-modified DNA sequences are nonselectively chemically attached to the surfaces of Au NPs at high densities, which may lead to the uncontrollable positioning and number of Au NPs in further assembly. Researchers have proposed multiple strategies to control the placement of DNA sequences at specific positions on Au NPs, thereby achieving the controllable assembly of Au NPs. Coughlin et al. proposed a light-mediated method to selectively release single-stranded DNA on the resonance region of the localized surface plasmon (LSP) from the surfaces of gold nanostars (AuNS) [3], followed by the functionalization of another thiol-DNA to this region, thereby achieving the functionalization of different DNA sequences at the main body and tip of the AuNS structure for the assembly of more complex structures. He et al. proposed a cold-driven approach that utilizes the repulsion of locally high concentrations of DNA by the crystallization of water molecules to precisely control the DNA coupling density on the surfaces of spherical gold nanoparticles (AuNPs) to obtain dimers, trimers and core-satellite structures [4]. The method is simple and requires only one step, without reagents such as salts, acids and surfactants, which can avoid complicated post-processing. In addition, anisotropic Au NPs with different coverage rates can be prepared by the eccentric encapsulation of Au NPs, and functionalization can be carried out in a site-specific way, achieving the specific and controllable modification of DNA [5]. Gibson et al. adopted this strategy to obtain anisotropic gold nanospheres and nanorods [6]. Then, they connected the two nanoparticles into dimers by the complementary hybridization of DNA strands with three-helical partial fragments. By adjusting the pH, the distance between nanoparticles can be changed, thereby achieving the regulation of the plasmonic coupling between dimers. In addition to regulating the surface coverage of Au NPs, bridging-mediated strategies have been used to guide the assembly of Au NPs. Zhang et al. designed a bridge DNA structure consisting of one double-stranded midsection and four single-stranded tails, and AuNPs could be connected with the single-stranded tails [7]. They achieved the dynamic regulation of one-step and multi-step reactions through toehold-mediated strand displacement reactions.
Due to the high cost of thiol-modified DNA, the use of poly-A DNA for functionalized Au NPs has received increasing attention. Ye et al. investigated the interaction between poly-A DNA and AuNP [8]. It was shown that, firstly, the loading density of DNA on the AuNP surface was almost independent of the length of poly-A. Secondly, compared with salt aging and low pH methods, freezing has higher biological interface stability. In addition, the formation of poly-A duplexes after freezing results in enhanced fluorescence. Based on these studies, the author utilized the freeze-driven assembly of plasmonic dimers using DNA with poly-A sequences at both ends. Fan and colleagues conducted an in-depth study on the role of ploy-A DNA in mediating the formation of AuNP assemblies. In 2020, they proposed a strategy for the patterning of gold nanoparticles [9]. They designed single-stranded encoders (SSEs) using specific single-stranded DNA containing poly-A sequences and synthesized a series of programmable atom-like nanoparticles (PANs) with precisely controllable valence states. Further, they designed specific assembly and hybridization reactions to prepare “colloidal molecules” with different sizes, compositions and chirality, and they realized bond breaking, bonding, rearrangement and logical operations through reversible reconstruction. The following year, they utilized the affinity between poly-A and the surfaces of AuNPs to extend anti-miRNA domains onto the surfaces of AuNPs to construct spherical nuclear acids (SNAs) [10]. By adjusting the length of poly-A to control the number and conformation of anti-miRNAs on AuNPs, and further assembling AuNP-anchored miRNAs, they evaluated the capture efficiency of SNAs with target miRNAs.

1.2. DNA Tile-Mediated Assembly

Self-assembly based on the DNA tile structure is one of the most important parts of structural DNA nanotechnology. Although designing DNA tiles typically only requires a few simple DNA strands, it is possible to assemble precise DNA nanostructures ranging from simple to complex. Additionally, the combination of functional materials with DNA nanostructures to form complexes with well-defined compositions and configurations will lead to new properties and applications [11]. As an example, Yu et al. reported a simple AuNP cluster-DNA nanocage hybrid assembly method [12]. They first constructed DNA tetrahedral and octahedral structures using DNA three-arm tiles or DNA four-arm tiles, respectively. Subsequently, the overhangs on a polyhedron hybridized with the complementary DNA-modified AuNPs allowed AuNPs to be anchored at specific locations to directly assemble AuNP tetramer–DNA tetrahedron hybrids and AuNP octamer–DNA octahedron structures.
In addition to individual DNA tile nanostructures, high-order assemblies of multiple DNA tile structures have also been used to guide the formation of Au NP multimers. He et al. used a DNA tetrahedron with a thiol-anchor constructed by four DNA single strands stoichiometrically conjugated with AuNPs, resulting in monovalent AuNPs [13]. Furthermore, monovalent AuNPs were used as building blocks to construct a specified number of high-order AuNP clusters through assembly. Tan et al. utilized the DNA tetrahedron structure to control the localization and alignment of AuNPs of three different sizes (5 nm, 10 nm, and 20 nm in diameter, respectively) to assemble a strongly coupled plasmonic core-satellite structure, which was called the TDN-based AuNP core-satellite plasmonic nanostructure (TetrAuCS) [14]. Feng et al. designed a DNA tetrahedron in which one edge was a single-stranded DNA aptamer that could recognize and respond to Hg2+. Three vertices of the DNA tetrahedron were anchored to a core AuNP with a diameter of 100 nm through Au-S bonds, and another vertex was connected to a satellite AuNP with a diameter of 20 nm through poly-A to construct a core-satellite nanostructure. This structure served as a SERS molecular-ruler to detect conformational changes under Hg2+ stimulation [15].
The functionalization of individual DNA strands at specific sites on the surfaces of nanoparticles can greatly improve the structural diversity. Pattern transfer strategies [16][17][18] can inherit the DNA molecular information encoded in the template with high fidelity, achieving control over the number, direction and length of functionalization on particles. Xie et al. demonstrated a three-molecular transfer strategy [19]. They first encapsulated a AuNP in a DNA icosahedron cage (I-Cage) template; then, the DNA strands predesigned in the nanocages could be covalently coupled to the AuNP surface through Au-S bonds. Subsequently, by removing the I-Cage template, the predesigned DNA patterns were transferred to the surfaces of AuNPs to obtain atomically equivalent DNA-printed nanoparticles (DPNPs) and further used for the assembly of satellite nanostructures.

1.3. DNA Origami-Mediated Assembly

DNA origami [20] is a technique that uses a long ssDNA called a scaffold and a set of short ssDNA called staples to construct DNA nanostructures. Each staple is unique and can be assembled to a specific position on the scaffold, which results in the addressability of DNA origami. Functional materials such as metal nanoparticles, quantum dots, fluorescent molecules and proteins can be positioned with nanoscale accuracy on DNA origami [21][22][23][24]. Furthermore, the arrangement of these functional materials on DNA origami is not limited to static systems, and the dynamic manipulation of functional materials in spatial and temporal can also be easily achieved [25], which expands the range of DNA-driven gold nanoparticle assemblies.
DNA origami has been widely used in static assembly systems for Au NPs. Yeşilyurt et al. constructed a meta-emitter that was composed of three AuNPs and a fluorophore [26]. They extended two groups of capture strands on one side of the triangular DNA origami, while they extended a third group of capture strands on the other side to assemble three AuNP assembly nanoantenna and obtained a gap of about 3 nm. Fluorophore ATTO 647N was positioned at the hotspot of the gap, and a plasmonic trimer nanoantenna driven by a single dye molecule was constructed to realize unidirectional meta-emitters. Martens et al. connected gold nanorods (AuNRs) on the two ends of a 3D DNA origami with a distance of 62 nm, forming a 90° heteromorphic nanorod–nanorod (NR-NR) chiral sample. A 40 nm gold nanosphere (AuNS) was attached in the middle of two AuNRs to form a nanorod–nanosphere–nanorod (NR-NS-NR) chiral structure [27]. These chiral arrangement structures could be treated as a coupled electron oscillator system that exhibited complex chiral optical fields, resulting in a strongly enhanced CD response.
In order to construct more complex assemblies of Au NPs, DNA origami is also used as assembly blocks to construct static high-order gold nanostructures. Liu et al. proposed a strategy for the 2D thin-layered chiral supramolecular self-assembly of programmable AuNRs guided by DNA origami hexamers [28]. They designed capture strands at defined positions on the triangular DNA origami and used specific connector strands to splice the DNA origami into different hexamer templates. AuNRs as building blocks were captured by the template-specified positions through the modified complementary DNA strands, constructing three types of bi-star and three types of pinwheel AuNR chiral supramolecular structures. The structures exhibited strong anisotropy and chiroptical responses. The following year, they adopted the same strategy to further create chiral core-satellite nanoparticle superstructures on triangular DNA origami hexamer templates by using one spherical gold nanoparticle as the core and six gold nanorods as satellites. A split or nonsplit circular dichroism (CD) line shape optical activity state was produced by the different conformation structures under light spin excitation [29]. In addition to the above strategy of specifically capturing gold nanoparticles on the templates of DNA origami higher-order structures, it is also a common method to assemble an individual DNA origami–gold nanoparticle composite structure as a building block before further assembling the high-order structure. For instance, Zhou et al. first assembled an AuNP in the cavity of a 3D hexagonal prism DNA origami (HDO) and then constructed symmetric or asymmetric AuNP multimers through orthogonal and directional bonding [30].
Introducing dynamic DNA assembly into structural systems can confer tailored optical properties to gold nanoparticle assemblies. Liu‘s group conducted an in-depth study. In 2019, they assembled multilayer sliding nanosystems by combining three DNA origami filaments with two AuNPs at different levels [31]. The sliding nanosystem could perform coordinated and reversible sliding motions driven by DNA fuel strands. Simultaneously, AuNPs can be used as optical probes to dynamically interact with fluorophores anchored on DNA origami to detect the sliding process in situ. In 2021, they designed a double-layer plate DNA origami template with a curved track fixed on the top of the plate to anchor a AuNR to the rotary module, and a AuNR walking module was assembled on the bottom surface of the plate [32]. Rotating and sliding motions were performed by toehold-mediated strand displacement reactions. In 2022, they designed a large DNA origami ring with an inner diameter of about 60 nm as the ring gear and a small DNA origami ring with an outer diameter of 30 nm as the sun gear; they then assembled two AuNPs with a diameter of 15 nm in the gap as the planet gears to form a rotary nanodevice [33]. Fluorescence spectra were used to record the optical rotation dynamics of the nanodevice in real time.
Similar to DNA tiles, DNA origami can also be used as a template to transfer patterns onto AuNPs. Niu et al. reported a DNA origami-based nanoprinting (DOBNP) strategy to transfer basic DNA strands of pre-determined sequence and location from triangular DNA origami to the surfaces of gold nanocubes (AuNCs) [34]. These DNA strands ensured a specificity connection between the AuNCs and AuNPs, resulting in the generation of a stereo-controlled AuNC–AuNP nanostructure (AANs) with a controlled composition and geometry. They anchored individual dye molecules in hotspot regions and detected the stronger amplification of surface-enhanced Raman scattering (SERS) signals due to significantly enhanced electromagnetic fields. The method provides an opportunity to fabricate stereo-controlled metallic nanostructures for the design of highly sensitive photonic devices. Additionally, Xiong et al. developed a method called molecular stamping (MOST) to pattern DNA-coated nanoparticles [35]. In this patterning process, the coordinated DNA frame acts as a molecular stamping apparatus (MOST App) that transfers and immobilizes a DNA sequence (named molecular “ink”) to the surface of the nanoparticle to form a presetted pattern. After the nanoparticles are treated by the MOST process, the surfaces of the nanoparticles have single-molecule “patches” as anisotropic “bonds” with different affinities. Further, these nanoparticles are assembled into predefined clusters whose structure is determined by the location of the patches.

2. Gold Nanoparticle Arrays

2.1. 1D Arrays

A typical procedure for preparing 1D arrays usually involves two processes: the assembly of DNA nanostructure templates and the localization of Au NPs. The essential aspect of the procedure lies in the design of stable DNA nanostructure templates. DNA nanostructures with repetitive units assembled by DNA bricks provide a favorable template foundation for 1D nanogold arrays. For instance, Liang et al. assembled 1D DNA structural templates using repeating units composed of three DNA strands, and they used it to assemble an ordered linear AuNP plasmonic nanostructure at the oil–water interface. This structure had excellent specificity for the detection of miRNA-155 [36]. Ren et al. designed three shorter ssDNA sequences (N1, N2 and N3) to fold with two longer ssDNA sequences (S1 and S2) to form a ribbon-like DNA nanostructure with repetitive rectangular units [37]. Five strands, including a capture sequence, N3, were mixed with complementary sequence-modified AuNPs to form 1D plasmonic gold metamaterials, which could produce enhanced Raman scattering. Golla et al. reported a helically twisted nanoribbon for the further assembly of AuNPs or AuNRs to fabricate 1D chiral plasmonic nanostructures [38]. Zhang et al. designed a complex DNA structure template [39]. They used double crossover (DX) tiles composed of five DNA strands as assembly units, and they designed sticky ends on both sides and ends to assemble bundles with an adjustable width and composition of 1D DNA bundles and large AuNPs.
Benefiting from the excellent programmability and addressability of DNA origami templates, Au NPs can be easily configured into 1D arrays. Wang et al. constructed a highly rigid 1D chain structure formed by DNA origami hashtag tile polymerization, which served as a frame for Au NPs assembly, and they precisely arranged a variety of microscale chiral and magnetic plasmonic polymers [40]. In addition to static assembly, dynamic structures have also been designed and fabricated. Johnson et al. designed and assembled a DNA origami hinge structure with a AuNP inside. When the temperature changed, the structure generated a thermal response, leading to a configuration transition [41]. Then, composite arrays of linear NPs and hinges with variable configurations were obtained by designing connections between the hinge arms and thermal actuator.

2.2. 2D Arrays

There are two effective traditional methods for the preparation of Au NP 2D arrays: one is to use bonding agents with specific interactions (such as DNA strands) as assembly media, and the other is to use patterns on the substrate as templates to limit the assembly of NPs. Given that DNA-AuNP superlattices extruded between SiNx windows and xTEM liquid cells can produce large amounts of 2D NPs, Shekhirev et al. produced large-area monolayer NP assemblies via the crystallization of a finite volume solution containing complementary DNA-functionalized NPs by weak interactions on a surface [42]. The 2D NP structure could respond to changes in solvent composition. Combining DNA self-assembly with lithography can produce functionalized 2D surfaces for the high-resolution assembly of nanoparticle arrays. Mirkin’s group patterned DNA on a gold-plated substrate using photolithography technology by placing DNA in pores constrained by a polymethyl methacrylate (PMMA) template; they then assembled 80 nm gold cubes with complementary DNA sequences in the holes and finally removed the PMMA template to obtain a 2D array of gold cubes [43]. Using a similar strategy, Myers et al. manufactured structurally reconfigurable metasurfaces of AuNRs [44]. They controlled the position and orientation of AuNRs by controlling the DNA functionalization pattern and drove the reconfiguration of the NP arrays based on the temperature dependence between the NPs and the ssDNA anchoring density.
However, the methods above require complex surface modification, which hinders their further application. Therefore, it is necessary to develop an effective strategy that does not require special surface treatment. In fact, DNA origami-guided assembly has demonstrated an unparalleled ability to organize metal nanoparticles precisely into their designed locations without special treatment. Shen et al. used DNA origami hexagons as building blocks to design and assemble honeycomb arrays or tubular high-order networks with sizes of up to a few micrometers [45]. Additionally, the addressability of the unit block allowed the researchers to precisely place the Au NPs at the specified positions and obtain DNA origami–nanoparticle composite blocks, which were further assembled to realize the construction of periodic gold nano-arrays. Similarly, Yang et al. assembled 1D and 2D AuNR array structures using cross-shaped DNA origami–AuNR composites as building blocks [46].
Bottom-up assembly based on DNA origami can also be combined with top-down lithography [47]. Martynenko et al. demonstrated a method for the precisely targeted placement of various shapes of DNA origami on the micrometer to millimeter scale [48]. They utilized two approaches of connector-mediated binding (hollow tubes) and direct binding (the tetrapod) through self-aligned binding to realize the upright positioning of various DNA origami shapes. As a proof of concept, they assembled the DNA origami structures with AuNPs and ultimately connected individually placed DNA origami with DNA pillars on an x-y plane to create continuous periodic networks.

2.3. 3D Lattices

Programmable DNA-mediated assembly provides a vast and diverse design space for 3D lattice construction, where the nanoparticle size, spacing and crystal symmetry can all be independently controlled. Mirkin’s group developed a method for the construction of lattices with programmable nanomaterials [49][50][51]. Functionalized nanoparticles act as “atoms” and oligonucleotides act as “bonds”, and they are assembled into crystal structures with an adjustable composition, symmetry and lattice parameters, by tightly controlling the assembly characteristics of these oligonucleotide–nanoparticle conjugates. In recent years, they have studied the properties of crystal structures by adjusting the design of DNA bonds based on this construction method. In 2020, they reported a new method for the synthesis of colloidal crystals using azobenzene modified photo-responsive DNA strands [52]. The photoisomerization of azobenzene molecules during UV and visible light switching can lead to the reversible assembly and decomposition of the nanoparticle lattice. By using ultraviolet light as a trigger signal, nanoparticles on colloidal crystal sheets can be selectively removed, enabling them to be photolithographed into specific shapes. In 2023, they designed a DNA dendrimer as a symmetry-breaking synthon to encode anisotropic and orthogonal interactions on individual colloidal particle building blocks, which broke the symmetry of colloidal crystals [53]. Moreover, they investigated the mechanical strength of metamaterials formed by the DNA-mediated assembly of different nanoparticles. They found that nanosolid, nanocage and nanoframe mechanical metamaterials with the same crystal symmetry exhibited significantly different specific stiffness and strength. In particular, the strength of the nanoframe lattice was about six times stronger than that of the nanosolid lattice [50].
DNA origami guides the controllable arrangement of nanoparticles in a programmable manner, and it has rapidly developed into an ideal method of constructing nanoparticle crystals. Tian’s group has performed a great deal of research in this direction. Firstly, since the vertices and internal cavities of the regular-octahedral DNA origami wireframe structure can be designed with specific connection sequences, AuNPs only need to be modified with complementary sequences, which can be loaded into the octahedral cavity. Drawing inspiration from the “node-and-spacer” construction approach of coordination polymers, they used the octahedral frameworks as “nodes” and ssDNA as “spacers”, and, by regulating the number and spatial positions of ssDNA extended from the vertices of the octahedral shells, the valences and directions of nanoparticles were designed, which was equivalent to achieving the “valence state” encoding of the internal AuNPs [54]. A variety of static and dynamic crystal structures [55][56][57] were obtained by the further assembly of the encoded structures. Secondly, they introduced an elongated octahedron framework to explore the co-crystallization of anisotropic heterogeneous species and realize the construction of composite superlattices [58][59][60]. Furthermore, DNA structures such as tetrahedrons and cubes were used as frames with valence. AuNPs of different sizes, quantum dots and proteins were loaded inside the frame as nano-objects, and a variety of ordered multivariate heterogeneous superlattices and different crystalline systems were constructed [61][62]. In addition to wireframe DNA origami, Lin et al. used a similar strategy to design and assemble 1D, 2D and 3D arrays by encoding “keys” on the three orthogonal axes of 3D semi-closed cuboid DNA nanochambers (DNCs) [63]. Julin et al. employed the high negative charge of the surface of a DNA origami to assemble a six-helix bundle DNA origami and cationic AuNPs into a 3D ordered superlattice [64].
Top-down lithography and bottom-up self-assembly techniques have also been shown to be useful for 3D lattice construction. The preparation of microarrays and the functionalization of the bottoms of pores are performed in the same manner as for the 2D arrays described above. Two groups of nanoparticles with complementary sequences were prepared and hybridized at room temperature. Under the limited template space, the gold nanoclusters were forced to merge and reorganize to produce a highly ordered single crystal superlattice. The orientation, position and size of the lattice could be controlled by the template holes and the assembly conditions [65].

This entry is adapted from the peer-reviewed paper 10.3390/s23229229

References

  1. Liang, L.; Zheng, P.; Zhang, C.; Barman, I. A Programmable DNA-Silicification-Based Nanocavity for Single-Molecule Plasmonic Sensing. Adv. Mater. 2021, 33, 2005133.
  2. Liu, H.-L.; Ahmed, S.A.; Jiang, Q.-C.; Shen, Q.; Zhan, K.; Wang, K. Gold Nanotriangle-Assembled Nanoporous Structures for Electric Field-Assisted Surface-Enhanced Raman Scattering Detection of Adenosine Triphosphate. ACS Sens. 2023, 8, 1280–1286.
  3. Coughlin, E.E.; Hu, J.; Lee, A.; Odom, T.W. Light-Mediated Directed Placement of Different DNA Sequences on Single Gold Nanoparticles. J. Am. Chem. Soc. 2021, 143, 3671–3676.
  4. He, M.Q.; Chen, S.; Yao, K.; Wang, K.; Yu, Y.L.; Wang, J.H. Oriented Assembly of Gold Nanoparticles with Freezing-Driven Surface DNA Manipulation and Its Application in SERS-Based MicroRNA Assay. Small Methods 2019, 3, 1900017.
  5. Zhu, R.; Feng, H.; Li, Q.; Su, L.; Fu, Q.; Li, J.; Song, J.; Yang, H. Asymmetric Core-Shell Gold Nanoparticlesand Controllable Assemblies for SERS Ratiometric Detection of MicroRNA. Angew. Chem. Int. Ed. 2021, 60, 12560–12568.
  6. Gibson, K.J.; Prominski, A.; Lee, M.S.; Cronin, T.M.; Parker, J.; Weizmann, Y. Discrete pH-Responsive Plasmonic Actuators via Site-Selective Encoding of Nanoparticles with DNA Triple Helix Motif. Cell Rep. Phys. Sci. 2020, 1, 100080.
  7. Zhang, J.N.; Yu, J.Y.; Jin, J.; Zhou, X.; Liang, H.J.; Zhou, F.; Jiang, W. Bridge DNA guided assembly of nanoparticles to program chemical reaction networks. Nanoscale 2022, 14, 12162–12173.
  8. Ye, Y.; Hou, S.; Wu, X.; Cheng, X.; He, S. Freeze-Driven Adsorption of Poly-A DNA on Gold Nanoparticles: From a Stable Biointerface to Plasmonic Dimers. Langmuir 2022, 38, 4625–4632.
  9. Yao, G.B.; Li, J.; Li, Q.; Chen, X.L.; Liu, X.G.; Wang, F.; Qu, Z.B.; Ge, Z.L.; Narayanan, R.P.; Williams, D.; et al. Programming nanoparticle valence bonds with single-stranded DNA encoders. Nat. Mater. 2020, 19, 781–788.
  10. Jiao, K.; Yan, Q.L.; Guo, L.J.; Qu, Z.B.; Cao, S.T.; Chen, X.L.; Li, Q.; Zhu, Y.; Li, J.; Wang, L.H.; et al. Compartmenting Poly-Adenine-Based Spherical Nucleic Acids for Efficient Live-Cell MicroRNA Capture. Angew. Chem. Int. Ed. 2021, 60, 14438–14445.
  11. Lu, Y.X.; Tan, Y.T.; Xiao, Y.; Li, Z.X.; Sheng, E.Z.; Dai, Z.H. A silver@ gold nanoparticle tetrahedron biosensor for multiple pesticides detection based on surface-enhanced Raman scattering. Talanta 2021, 234, 122585.
  12. Yu, Y.; Lei, Y.X.; Dong, Q.; Li, Y.L. Functionalization of Tile-based DNA Nanocages with Gold Nanoparticles (AuNPs) to Form AuNP Cluster-DNA Cage Hybrids. ChemNanoMat 2020, 6, 1175–1178.
  13. He, W.; Zhao, Y.; Xing, S.; Zhang, Y.; Wang, L.; Liu, H. DNA Tetrahedron Framework Guided Conjugation and Assembly of Gold Nanoparticles. ChemPlusChem 2022, 87, e202200159.
  14. Tan, Y.; Zhou, J.X.; Xing, X.T.; Wang, J.R.; Huang, J.K.; Liu, H.Y.; Chen, J.J.; Dong, M.J.; Xiang, Q.; Dong, H.F.; et al. DNA Assembly of Plasmonic Nanostructures Enables In Vivo SERS-Based MicroRNA Detection and Tumor Photoacoustic Imaging. Anal. Chem. 2023, 95, 11236–11242.
  15. Feng, N.; Zhang, L.; Shen, J.; Hu, Y.; Wu, W.; Kouadio Fodjo, E.; Chen, S.; Huang, W.; Wang, L. SERS molecular-ruler based DNA aptamer single-molecule and its application to multi-level optical storage. Chem. Eng. J. 2022, 433, 133666.
  16. Rizzuto, F.J.; Trinh, T.; Sleiman, H.F. Molecular Printing with DNA Nanotechnology. Chem 2020, 6, 1560–1574.
  17. Liang, L.; Wu, L.; Zheng, P.; Ding, T.; Ray, K.; Barman, I. DNA-Patched Nanoparticles for the Self-Assembly of Colloidal Metamaterials. JACS Au 2023, 3, 1176–1184.
  18. Edwardson, T.G.W.; Lau, K.L.; Bousmail, D.; Serpell, C.J.; Sleiman, H.F. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles. Nat. Chem. 2016, 8, 162–170.
  19. Xie, N.L.; Liu, S.Y.; Fang, H.M.; Yang, Y.J.; Quan, K.; Li, J.; Yang, X.H.; Wang, K.M.; Huang, J. Three-Dimensional Molecular Transfer from DNA Nanocages to Inner Gold Nanoparticle Surfaces. ACS Nano 2019, 13, 4174–4182.
  20. Rothemund, P.W.K. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440, 297–302.
  21. Anderson, N.T.; Ren, S.K.; Chao, J.; Dinolfo, P.H.; Wang, X. Exploiting Plasmon-Mediated Energy Transfer to Enhance End-to-End Efficiency in a DNA Origami Energy Transfer Array. ACS Appl. Nano Mater. 2019, 2, 5563–5572.
  22. Dickinson, G.D.; Mortuza, G.M.; Clay, W.; Piantanida, L.; Green, C.M.; Watson, C.; Hayden, E.J.; Andersen, T.; Kuang, W.; Graugnard, E.; et al. An alternative approach to nucleic acid memory. Nat. Commun. 2021, 12, 2371.
  23. Peil, A.; Zhan, P.F.; Duan, X.Y.; Krahne, R.; Garoli, D.; Liz-Marzan, L.M.; Liu, N. Transformable Plasmonic Helix with Swinging Gold Nanoparticles. Angew. Chem. Int. Ed. 2022, 62, e202213992.
  24. Hellmeier, J.; Platzer, R.; Mühlgrabner, V.; Schneider, M.C.; Kurz, E.; Schütz, G.J.; Huppa, J.B.; Sevcsik, E. Strategies for the Site-Specific Decoration of DNA Origami Nanostructures with Functionally Intact Proteins. ACS Nano 2021, 15, 15057–15068.
  25. Zhan, P.F.; Urban, M.J.; Both, S.; Duan, X.Y.; Kuzyk, A.; Weiss, T.; Liu, N. DNA-assembled nanoarchitectures with multiple components in regulated and coordinated motion. Sci. Adv. 2019, 5, eaax6023.
  26. Yeşilyurt, A.T.M.; Sanz-Paz, M.; Zhu, F.; Wu, X.; Sunil, K.S.; Acuna, G.P.; Huang, J.-S. Unidirectional Meta-Emitters Based on the Kerker Condition Assembled by DNA Origami. ACS Nano 2023, 17, 19189–19196.
  27. Martens, K.; Binkowski, F.; Nguyen, L.; Hu, L.; Govorov, A.O.; Burger, S.; Liedl, T. Long- and short-ranged chiral interactions in DNA-assembled plasmonic chains. Nat. Commun. 2021, 12, 2025.
  28. Liu, Y.; Ma, L.; Jiang, S.X.; Han, C.; Tang, P.; Yang, H.; Duan, X.Y.; Liu, N.; Yan, H.; Lan, X. DNA Programmable Self-Assembly of Planar, Thin-Layered Chiral Nanoparticle Superstructures with Complex Two-Dimensional Patterns. ACS Nano 2021, 15, 16664–16672.
  29. Ma, L.; Liu, Y.; Han, C.; Movsesyan, A.; Li, P.; Li, H.; Tang, P.; Yuan, Y.; Jiang, S.; Ni, W.; et al. DNA-Assembled Chiral Satellite-Core Nanoparticle Superstructures: Two-State Chiral Interactions from Dynamic and Static Conformations. Nano Lett. 2022, 22, 4784–4791.
  30. Zhou, Y.H.; Dong, J.Y.; Zhou, C.; Wang, Q.B. Finite Assembly of Three-Dimensional DNA Hierarchical Nanoarchitectures through Orthogonal and Directional Bonding. Angew. Chem. Int. Ed. 2022, 61, e202116416.
  31. Zhan, P.F.; Both, S.; Weiss, T.; Liu, N. DNA-Assembled Multilayer Sliding Nanosystems. Nano Lett. 2019, 19, 6385–6390.
  32. Xin, L.; Duan, X.Y.; Liu, N. Dimerization and oligomerization of DNA-assembled building blocks for controlled multi-motion in high-order architectures. Nat. Commun. 2021, 12, 3207.
  33. Peil, A.; Xin, L.; Both, S.; Shen, L.Y.; Ke, Y.G.; Weiss, T.; Zhan, P.F.; Liu, N. DNA Assembly of Modular Components into a Rotary Nanodevice. ACS Nano 2022, 16, 5284–5291.
  34. Niu, R.J.; Song, C.Y.; Gao, F.; Fang, W.N.; Jiang, X.Y.; Ren, S.K.; Zhu, D.; Su, S.; Chao, J.; Chen, S.F.; et al. DNA Origami-Based Nanoprinting for the Assembly of Plasmonic Nanostructures with Single-Molecule Surface-Enhanced Raman Scattering. Angew. Chem. Int. Ed. 2021, 60, 11695–11701.
  35. Xiong, Y.; Yang, S.Z.; Tian, Y.; Michelson, A.; Xiang, S.T.; Xin, H.L.; Gang, O. Three-Dimensional Patterning of Nanoparticles by Molecular Stamping. ACS Nano 2020, 14, 6823–6833.
  36. Liang, H.; Jiang, L.; Li, H.; Zhang, J.; Zhuo, Y.; Yuan, R.; Yang, X. DNA-Guided One-Dimensional Plasmonic Nanostructures for the SERS Bioassay. ACS Sens. 2023, 8, 1192–1199.
  37. Ren, S.K.; Wang, J.; Song, C.Y.; Li, Q.; Yang, Y.J.; Teng, N.; Su, S.; Zhu, D.; Huang, W.; Chao, J.; et al. Single-Step Organization of Plasmonic Gold Metamaterials with Self-Assembled DNA Nanostructures. Research 2019, 2019, 7403580.
  38. Golla, M.; Albert, S.K.; Atchimnaidu, S.; Perumal, D.; Krishnan, N.; Varghese, R. DNA-Decorated, Helically Twisted Nanoribbons: A Scaffold for the Fabrication of One-Dimensional, Chiral, Plasmonic Nanostructures. Angew. Chem. Int. Ed. 2019, 58, 3865–3869.
  39. Zhang, Y.L.; Yang, D.L.; Wang, P.F.; Ke, Y.G. Building Large DNA Bundles via Controlled Hierarchical Assembly of DNA Tubes. ACS Nano 2023, 17, 10486–10495.
  40. Wang, P.F.; Huh, J.H.; Park, H.; Yang, D.L.; Zhang, Y.W.; Zhang, Y.L.; Lee, J.; Lee, S.; Ke, Y.G. DNA Origami Guided Self-Assembly of Plasmonic Polymers with Robust Long-Range Plasmonic Resonance. Nano Lett. 2020, 20, 8926–8932.
  41. Johnson, J.A.; Dehankar, A.; Winter, J.O.; Castro, C.E. Reciprocal Control of Hierarchical DNA Origami-Nanoparticle Assemblies. Nano Lett. 2019, 19, 8469–8475.
  42. Shekhirev, M.; Sutter, E.; Sutter, P. In Situ Atomic Force Microscopy of the Reconfiguration of On-Surface Self-Assembled DNA-Nanoparticle Superlattices. Adv. Funct. Mater. 2019, 29, 1806924.
  43. Zheng, C.Y.; Palacios, E.; Zhou, W.J.; Hadibrata, W.; Sun, L.; Huang, Z.Y.; Schatz, G.C.; Aydin, K.; Mirkin, C.A. Tunable Fluorescence from Dye-Modified DNA-Assembled Plasmonic Nanocube Arrays. Adv. Mater. 2019, 31, 1904448.
  44. Myers, B.D.; Palacios, E.; Myers, D.I.; Butun, S.; Aydin, K.; Dravid, V.P. Stimuli-Responsive DNA-Linked Nanoparticle Arrays as Programmable Surfaces. Nano Lett. 2019, 19, 4535–4542.
  45. Shen, L.Y.; Pan, V.; Li, H.F.; Zhang, Y.L.; Wang, P.F.; Ke, Y.G. Programmable assembly of gold nanoparticle nanoclusters and lattices. J. Mater. Chem. B 2020, 8, 6810–6813.
  46. Yang, S.; Liu, W.Y.; Zhang, Y.W.; Wang, R.S. Bottom-Up Fabrication of Large-Scale Gold Nanorod Arrays by Surface Diffusion-Mediated DNA Origami Assembly. ACS Appl. Mater. Interfaces 2021, 13, 50516–50523.
  47. Wang, Z.H.; Liu, Z.; Dempwolf, W.; Molle, J.; Kanehira, Y.; Kogikoski, S.; Etzkorn, M.; Bald, I.; Stosch, R.; Wundrack, S. Surface-Enhanced Raman Spectroscopy on Selectively Adsorbed Plasmonic Nanostructures Using Polar Surface Arrays. ACS Appl. Nano Mater. 2023, 6, 14645–14655.
  48. Martynenko, I.V.; Erber, E.; Ruider, V.; Dass, M.; Posnjak, G.; Yin, X.; Altpeter, P.; Liedl, T. Site-directed placement of three-dimensional DNA origami. Nat. Nanotechnol. 2023, 1–7.
  49. Lee, S.; Zheng, C.Y.; Bujold, K.E.; Mirkin, C.A. A Cross-Linking Approach to Stabilizing Stimuli-Responsive Colloidal Crystals Engineered with DNA. J. Am. Chem. Soc. 2019, 141, 11827–11831.
  50. Li, Y.; Jin, H.; Zhou, W.; Wang, Z.; Lin, Z.; Mirkin, C.A.; Espinosa, H.D. Ultrastrong colloidal crystal metamaterials engineered with DNA. Sci. Adv. 2023, 9, eadj8103.
  51. Xiong, Q.S.; Lee, O.S.; Mirkin, C.A.; Schatz, G. Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State. J. Am. Chem. Soc. 2023, 145, 706–716.
  52. Zhu, J.H.; Lin, H.X.; Kim, Y.; Yang, M.W.; Skakuj, K.; Du, J.S.S.; Lee, B.; Schatz, G.C.; Van Duyne, R.P.; Mirkin, C.A. Light-Responsive Colloidal Crystals Engineered with DNA. Adv. Mater. 2020, 32, 1906600.
  53. Distler, M.E.; Landy, K.M.; Gibson, K.J.; Lee, B.; Weigand, S.; Mirkin, C.A. Symmetry-Breaking Dendrimer Synthons in Colloidal Crystal Engineering with DNA. J. Am. Chem. Soc. 2023, 145, 841–850.
  54. Wang, M.Y.; Dai, L.Z.; Duan, J.L.; Ding, Z.Y.; Wang, P.; Li, Z.; Xing, H.; Tian, Y. Programmable Assembly of Nano-architectures through Designing Anisotropic DNA Origami Patches. Angew. Chem. Int. Ed. 2020, 59, 6389–6396.
  55. Ma, N.N.; Dai, L.Z.; Chen, Z.; Ji, M.; Wang, Y.; Tian, Y. Environment-Resistant DNA Origami Crystals Bridged by Rigid DNA Rods with Adjustable Unit Cells. Nano Lett. 2021, 21, 3581–3587.
  56. Wang, Y.; Yan, X.H.; Zhou, Z.Y.; Ma, N.N.; Tian, Y. pH-Induced Symmetry Conversion of DNA Origami Lattices. Angew. Chem. Int. Ed. 2022, 61, e202208290.
  57. Yan, X.H.; Wang, Y.; Ma, N.N.; Yu, Y.F.; Dai, L.Z.; Tian, Y. Dynamically Reconfigurable DNA Origami Crystals Driven by a Designated Path Diagram. J. Am. Chem. Soc. 2023, 145, 3978–3986.
  58. Ji, M.; Liu, J.L.; Dai, L.Z.; Wang, L.; Tian, Y. Programmable Cocrystallization of DNA Origami Shapes. J. Am. Chem. Soc. 2020, 142, 21336–21343.
  59. Ji, M.; Zhou, Z.Y.; Cao, W.H.; Ma, N.N.; Xu, W.G.; Tian, Y. A universal way to enrich the nanoparticle lattices with polychrome DNA origami “homologs”. Sci. Adv. 2022, 8, eadc9755.
  60. Wang, Y.; Dai, L.Z.; Ding, Z.Y.; Ji, M.; Liu, J.L.; Xing, H.; Liu, X.G.; Ke, Y.G.; Fan, C.H.; Wang, P.; et al. DNA origami single crystals with Wulff shapes. Nat. Commun. 2021, 12, 3011.
  61. Dong, Y.X.; Liu, J.L.; Lu, X.Z.; Duan, J.L.; Zhou, L.Q.; Dai, L.Z.; Ji, M.; Ma, N.N.; Wang, Y.; Wang, P.; et al. Two-Stage Assembly of Nanoparticle Superlattices with Multiscale Organization. Nano Lett. 2022, 22, 3809–3817.
  62. Tian, Y.; Lhermitte, J.R.; Bai, L.; Vo, T.; Xin, H.L.L.; Li, H.L.; Li, R.P.; Fukuto, M.; Yager, K.G.; Kahn, J.S.; et al. Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels. Nat. Mater. 2020, 19, 789–796.
  63. Lin, Z.W.; Emamy, H.; Minevich, B.; Xiong, Y.; Xiang, S.T.; Kumar, S.; Ke, Y.G.; Gang, O. Engineering Organization of DNA Nano-Chambers through Dimensionally Controlled and Multi-Sequence Encoded Differentiated Bonds. J. Am. Chem. Soc. 2020, 142, 17531–17542.
  64. Julin, S.; Korpi, A.; Nonappa; Shen, B.X.; Liljestrom, V.; Ikkala, O.; Keller, A.; Linko, V.; Kostiainen, M.A. DNA origami directed 3D nanoparticle superlattice via electrostatic assembly. Nanoscale 2019, 11, 4546–4551.
  65. Wong, A.M.; Je, K.; Zheng, C.Y.; Jibril, L.; Miao, Z.Y.; Glotzer, S.C.; Mirkin, C.A. Arrays of Colloidal Single Crystals Engineered with DNA in Lithographically Defined Microwells. Nano Lett. 2023, 23, 116–123.
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