WO2024186458A2 - Rapid and scalable solution-based fabrication of quantum dot and quantum rod 2d arrays using dna origami - Google Patents

Abstract

Ultrafast methods to prepare high-density DNA functionalized nanoparticles using solution-based fabrication and application to aligned 2D QR lattices with nanometer scale spatial accuracy are described.

Description

RAPID AND SCALABLE SOLUTION-BASED FABRICATION OF QUANTUM DOT AND QUANTUM ROD 2D ARRAYS USING

DNA ORIGAMI

CLAIM OF PRIORITY

[0001] This application claims priority to U.S. Provisional Patent Application No. 63/485,855, filed February 17, 2023, which is incorporated by reference in its entirety.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

[0002] This invention was made with government support under CCF 1956054 awarded by the National Science Foundation, W91 INF- 19-2-0026 awarded by the Army Research Office, N00014-21-1-4013 awarded by the Office ofNaval Research, and FA9550-23-1-0210 awarded by the Air Force Office of Scientific Research. The government has certain rights in the invention.

FIELD OF THE INVENTION

[0003] The invention relates to an ultrafast method to prepare high-density DNA functionalized quantum dots (QDs) and quantum rods (QRs) using solution-based fabrication and application to aligned 2D QR lattices with nanometer scale spatial accuracy.

REFERENCE TO THE SEQUENCE LISTING

[0004] This application contains a Sequence Listing which has been submitted electronically in XML format and which is hereby incorporated by reference in its entirety. The XML copy, created on February 15, 2024, is named “RAPID AND SCALABLE SOLUTION-BASED FABRICATION.xml” and is 3,435 bytes in size. BACKGROUND

[0005] QDs and QRs have attracted extensive interest recently in the wake of their successful application in the electronic display industry [1-3], The commercialization of QD enhancement film (QDEF) has significantly improved the color range of traditional liquid-crystal display (LCD) TVs [4], Evidently, QD/QR-based devices are key players in next-generation displays [5, 6], especially in the field of micro-light-emitting-diodes (p-LEDs) due to their short emission linewidth and near unity quantum yield [7, 8], Quantum rods are particularly interesting because of their polarized light emission [9], and are promising candidates to improve the optical efficiency of display equipment significantly [10, 11], High-quality polarized light sources with QRs require the alignment of QRs along their long axes at the nano-to-micro scale [10], Previously reported alignment methods controlled the assembly of QRs with macroscale external forces or polymer matrices [10-12], which offered some extent of global control over the QR orientation but lacked the capability of local addressability of individual QRs and their interparticle distances. Evidence suggests that QDs/QRs lacking interparticle distance control suffer from “self-quenching” when they are deposited as thin films [13], which result from Forster resonant energy transfer (FRET) of excitons within the inhomogeneous size distribution [14], These drawbacks can be of paramount importance for advanced display applications such as virtual reality (VR) and augmented reality (AR) devices with p-LEDs where pixel sizes are only a few microns or less [7],

SUMMARY

[0006] Here, we developed an ultrafast dehydration-assisted one-step functionalization method to conjugate a dense layer of DNA ligands to QDs and QRs from their original organic solvent to aqueous buffers, which tremendously shortens the manufacturing time required for DNA-functionalized QDs/QRs (DNA-QDs/QRs) from a few days to a few minutes. This approach can be applied to QDs and QRs with various sizes, aspect ratio, spectra as well as shell surfaces. Moreover, synthesized DNA-QDs/QRs (dQD/dQRs) possess record-high DNA density on QDs/QRs, which endows them with excellent stability in a variety of salted aqueous buffers, as well as outstanding binding affinity and fidelity to DNA origami structures. Consequently, dQRs can align along the 6HB edge of a wireframe origami with high yield through DNA hybridization to aligned binding sites, whereas QRs fabricated on DNA origami via traditional routes suffer from low binding efficiency and no alignment on the origami. Moreover, we report a Surf ace- Assisted Large-Scale Assembly (SALSA) method to construct 2D origami lattices directly on a solid substrate to template aligned 2D QR lattice superstructures. We overcame the limitation of previous approaches by introducing sequence-specific lateral anti-parallel crossovers on the edges of the 6HB wireframe origami structures, which, for the first time, enabled the fabrication of 2D origami arrays with full control over orientation and 2D lattice type. The presented method circumvents the problematic issue of transferring solution-assembled DNA structures onto solid substrates, and further maintains lattice structures together with the templated nanomaterial arrangement and function after drying, achieving 2D QR arrays with orientation and inter- nanoparticle spacing control.

[0007] In one aspect, a method of forming a DNA functionalized complex can include mixing thiolated DNA with a plurality of an inorganic moiety in an organic solvent to form a mixture and dehydrating the mixture to form DNA functionalized complex. The thiolated DNA can be in an aqueous suspension.

[0008] In certain circumstances, recovering the DNA functionalized complex can include rehydrating the DNA functionalized complex. In certain circumstances, recovering the DNA functionalized complex can include resuspending the DNA functionalized complex. For example, a method can include dispersing of DNA and inorganic moiety to form the mixture, dehydrating the mixture, and rehydrating (recovering) the DNA functionalized inorganic moiety. Dispersing can include ultrasonic dispersing. In certain circumstances, thiolated DNA in aqueous buffer can be dehydrated and condensed on a surface of the inorganic moiety.

[0009] In certain circumstances, the thiolated DNA can be in an aqueous suspension when it is added to the organic solvent containing the inorganic moiety.

[0010] In certain circumstances, the DNA functionalized complex can be a DNA functionalized inorganic moiety.

[0011] In another aspect, a method of forming a 2D nanoparticle array can include tiling a plurality of DNA functionalized inorganic moi eties on a surface in a regular controlled pattern.

[0012] In another aspect, an array can include a plurality of nanoparticles aligned in a monolayer 2D array with a controlled spacing between each nanoparticle arising from a DNA origami lattice on a substrate.

[0013] In another aspect, a method of fabricating controlled arrays on a two dimensional (2D) solid surface can include preparing a substrate to include a pattern of shapes, and depositing a plurality of DNA origami structures in the pattern of shapes. In certain circumstances, the pattern of shapes can be formed with a mask material. In certain circumstances, the method can include forming the shapes in the mask material. In certain circumstances, the method can include etching an exposed area of the shape on the substrate. In certain circumstances, the method can include removing the mask material after depositing the DNA origami structures. In certain circumstances, the method can include exposing the deposited DNA origami structures in the pattern of shapes to a nanocrystal material having an affinity for the DNA origami structures. In certain circumstances, the method can include depositing the plurality of DNA origami structures in the pattern of shapes includes exposing the structures to a solution including a monovalent cation. The plurality of DNA origami structures can have one or more geometries that match with one or more shapes of the pattern of shapes.

[0014] In certain circumstances, dehydrating the mixture can include adding an alcohol to the mixture. The mixture can be a suspension.

[0015] In certain circumstances, the alcohol can include a C1-C8 alcohol, for example, C1-C8 alcohol is 1 -butanol.

[0016] In certain circumstances, the inorganic moiety can include a metal complex, a nanosphere, nanorod or other nanoshape. For example, the nanoparticle can be a semiconductor nanocrystal.

[0017] In certain circumstances, the inorganic moiety can include a nanoparticle having a size of less than 50 nm, less than 40 nm, less than 30 nm, less than 20 nm, or less than 10 nm.

[0018] In certain circumstances, tiling can include assembling DNA functionalized nanoparticles in a controlled orientation on the surface.

[0019] In certain circumstances, the array can include a wireframe DNA origami structure or assembly of multiple DNA origami structures.

[0020] In certain circumstances, the wireframe DNA origami structure can include a crossover design or hybridization or base-stacking or other interfacial self-assembly design. For example, the crossover design can permit selection of surface diffusion, error correction, face selection or combinations thereof.

[0021] In certain circumstances, the nanoparticles can be assembled to origami lattices with controlled positions, inter-particle distances and orientations.

[0022] In certain circumstances, the origami lattices with controlled positions can have a programmable and specified loading yield over 50%, over 60%, over 70%, over 80%, or over 90%.

[0023] In certain circumstances, the array can include a monolayer of nanoparticle faceselecting overhangs.

[0024] In certain circumstances, the array can include rhombic, square, scalene triangle, isosceles triangle, equilateral triangle, rectangular, trapezoid, pentagonal, hexagonal, heptagonal, or octagonal DNA origami, or DNA origami structures.

[0025] In certain circumstances, the DNA origami can self-assemble into a 2D lattice face up.

[0026] In certain circumstances, the controlled pattern can self-assemble either randomly or due to electrostatic interactions or DNA hybridization interactions between the surface and an origami or other affinity reagent, or by steric or other non-specific interactions that can induce face-up self-assembly.

[0027] In certain circumstances, the method can include annealing the array.

[0028] In certain circumstances, annealing the array can include thermally annealing either with or without mechanical or other vibration or shaking to enhance self-assembly kinetics and/or yield.

[0029] In certain circumstances, the inorganic moiety can include a nanoparticle, which can be a semiconductor nanoparticle (for example, a quantum dot and quantum rod). Each nanoparticle can be, for example, gold, InP, CdSe, CdTe, CdS, ZnS, ZnSe, Ag2Te, AgzSe, Ag2S, PbS, PbSe, CdSe/CdS core/shell, CdSe/ZnS core/shell, ZnSe/ZnS core/shell, alloyed CdSeS, alloyed CdSeTe, or alloyed CdZnSe.

[0030] Other aspects, embodiments, and features will be apparent from the following description, the drawings, and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0031] FIG. l is a schematic of workflow to prepare dehydration-assisted DNA conjugation to QDs (dQDs) and QRs (dQRs).

[0032] FIG. 2A shows TEM and size distribution of QD600, QD660, QR560, and QR620. FIG. 2B shows photoluminescence (PL) spectra of thiolated DNA labeled with FAM in various concentration. FIG. 2C shows a FAM fluorescence calibration curve calculated from FIG. 2B (x=(y+29450)/442, 7?²=0.99916). FAM was excited at 485 nm. FIG. 2D shows DNA loading density of various QDs and QRs with literature method (yellow) and the dehydration-assisted conjugation (green).

[0033] FIG. 3A shows an AGE image of dQD660 prepared with or without NaOH, TOPO, and TBAB. FIG. 3B shows an AGE image of dQD660 with various 1 -butanol/water ratio. FIG. 3C shows an AGE image of dQD660 prepared with various dehydration time (Ctrl: mQD660).

[0034] FIG. 4A is a schematic of hybridization efficiency of dQD/QR and mQD/QR. FIG. 4B shows the extinction coefficient (dash-dotted line) and photoluminescence (PL) spectra (solid line) of QD600, QD660, QR560, QR620, and Cy5. FIG. 4C shows FRET efficiencies as a function of acceptors calculated theoretically (dash-dotted curves), and from QD/QR emission intensities. Representative PL spectra of d) QD600-Cy5, e) QD660-Cy5, f) QR560-Cy5, and g) QR620-Cy5

FRET pairs. [0035] FIG. 5 shows schematic and representative TEM of loading efficiency and alignment efficiency of dQR620/mQR620-origami and dQD660/mQD660-origami assemblies. Scale bar: 50 nm.

[0036] FIGS. 6A-6C show crossover design on a rhombic origami for 2D lattice superstructures. FIG. 6A shows two 8nt extensions are introduced to two neighboring edges respectively (solid squares and circles) with unique DNA sequences that hybridize to the two vacancies introduced in their parallel edges (hollow squares and circles). FIG. 6B shows origami with crossovers can assemble into hexagonal 2D lattices in solution and then transferred to a substrate. FIG. 6C shows TEM images showing aggregation and layered species of 2D origami lattice sample prepared via dropcast post assembly in solution. Scale bars: 200 nm.

[0037] FIGS. 7A-7F show surface-assisted large-scale assembly of QR binding origami. FIG. 7A shows 5 binding DNA overhangs (red) are introduced to the long axis of the origami to anchor QRs-DNA with complementary sequences along the axis. Lateral crossover strands are omitted from all illustrations. FIG. 7B shows the origamis can land on the mica substrate facing up (white) or down (cyan). Each species assembles into separate lattices. FIG. 7C shows dry AFM images of SALSA with the rhombic origami design in FIG. 7A. Origami array landed on different side is indicated with an arrow. FIG. 7D shows face-selecting overhangs are introduced to the side of the binding strands to avoid binding strand facing down on mica. FIG. 7E shows face-selecting rhombic origami only assemble into 2D lattices facing up. FIG. 7F shows dry AFM images of SALSA with the Face-selecting rhombic origami. Scale bars: 600 nm (c top and f top) and 200 nm (c bottom and f bottom).

[0038] FIGS. 8A-8E show aligned QR 2D array templated by SALSA origami lattice. FIG. 8A shows schematic illustration of the fabrication of aligned QR 2D array using rhombic origami with or without crossovers. FIG. 8A shows an overview AFM image (left) and orientation distribution (right) of QR 2D array using rhombic origami with crossovers. FIG. 8C shows a zoomed-in area (left) from FIG. 8C and QR orientation distribution (right). FIG. 8D shows an overview AFM image (left) and orientation distribution (right) of QR-origami assemblies using rhombic origami without crossovers showing random orientation. FIG. 8E shows a zoomed-in area (left) from FIG. 8D and orientation distribution (right) showing random origami and QR arrangement. Scale bar: 600 nm for FIG. 8B and FIG. 8D, 200 nm for FIG. 8C and FIG. 8E.

[0039] FIG. 9A shows the dehydrati on-rehydration method to synthesize various dense-DNA functionalized QDs/QRs. FIG. 9B shows templating QDs/QRs into aligned monolayer 2D arrays with DNA origami lattices on a substrate.

[0040] FIG. 10A shows a schematic of the workflow to prepare dehydration-assisted high- density ssDNA conjugated InP/ZnS QD. FIG. 10B depicts the extinction coefficient and FIG. 10C depicts the photoluminescence (PL) spectra of InP/ZnS QD53O, InP/ZnS QD590, InP/ZnS QD620, and InP/ZnS QD650.

[0041] FIGS. 11A-11F depict the Cavity-Shape Modulated Origami Placement (CSMOP) method. FIG. 11A shows a schematic illustration of the CSMOP method. Step i shows a silicon substrate with a 90 nm thick silica layer; step ii shows a TMS coating; step iii shows a PMMA resist coating; step iv shows EBL and resist development; step v shows O2 plasma etching; step vi shows origami placement; and step vii shows PMMA lift-off. FIG. 1 IB depicts the design and AFM image of the rhombic origami with one side modified with ssDNA overhangs with a binding sequence and the remaining 20 being thymidine (20T). FIG. 11C depicts an AFM image of a rhombic shaped cavity array after O2 plasma etching. FIG. 1 ID depicts an ATM image of rhombic origamis placed at the bottom of the cavities. FIG. 1 IE depicts AFM image of the origami array after PMMA lift-off. FIG. 1 IF depicts design and AFM images of a square-shaped origami placement with the CSMOP method.

[0042] FIGS. 12A-12C depict AFM images of the cavities after rhombic origami placement. Origamis were located at the bottom of the cavities with no origami binding on the resist as evidenced by different channels of the AFM image: FIG. 12A shows height channel; FIG. 12B shows height channel with the height color scale shifted to the bottom of the cavities; FIG. 12C shows phase channel.

[0043] FIGS. 13A-13F depict the influence of cavity size and cation on origami placement yield and orientation control. FIG. 13A shows AFM images of rhombic shape cavity arrays fabricated with Dose 1 (670 pC/cm², i), Dose 2 (868 pC/cm², ii) and Dose 3 (1132 pC/cm², iii). FIG. 13B shows AFM images of rhombic origami arrays fabricated with CSMOP using cavity arrays of corresponding sizes (i— iii). FIG. 13C shows the percentage of cavity sites with an intact origami monomer (bottom), multiple origamis at one site (middle) and other DNA structures (top) in CSMOP arrays in FIG. 13B. FIG. 13D shows rhombic origami orientation (long diagonal axis) angle distribution in array i and ii in FIG. 13B. FIG. 13E shows AFM images of the cavity array (Dose 1) with rhombic cavities oriented at -45° or 45° (top) and the origami array produced (middle), with the origami orientation angle distribution (bottom). FIG. 13F shows CSMOP arrays produced using 100 mM Na⁺ in the placement buffer, with corresponding cavity sizes (i— iii). Placement yields of intact origami monomers in CSMOP arrays are annotated on AFM images.

[0044] FIGS. 14A-14B depict AFM images of cavities fabricated with various EBL doses. FIGS. 14A shows AFM images and measured dimensions of the cavities after resist development and before O2 plasma etching. FIG. 14B shows AFM images and measured dimensions of the cavities after O2 plasma etching.

[0045] FIGS. 15A-15B depict CSMOP with 100 mM Na FIG. 15A shows AFM images of CSMOP arrays fabricated with various cavity sizes in FIG. 13A, i-iii. Indicated segments marked the orientation of the origami, generated by the orientation analysis code. FIG. 15B shows the corresponding origami orientation angle distribution.

[0046] FIGS. 16A-16E depict CSMOP array of rhombic origamis templating gold nanorod (AuNRs) for orientation dependent plasm onic light scattering. FIG. 16A shows a schematic illustration of DNA functionalized AuNR hybridization to CSMOP array. FIG. 16B shows an AFM image of AuNRs templated by the CSMOP array with vertical orientations. FIG. 16C shows dark-field microscope (50 W halogen lamp) image of CSMOP array templated AuNRs with a vertical analyzer direction. Strips i and ii are arrays of origamis oriented vertically with interorigami distance of 500 nm and 250 nm, respectively; strips iii and iv are arrays of origamis oriented horizontally with inter-origami distance of 250 nm and 500 nm, respectively. FIG. 16D shows corresponding AFM images of CSMOP array templated AuNRs in strips i-iv. FIG. 16E shows dark-field microscope images of CSMOP templated AuNR array under polarized incident light. Incident light polarization angle: 0° (left), 45° (middle), 90° (right). AuNR appears red or green when the incident light is polarized parallel or perpendicular to the long axis of the AuNR respectively.

[0047] FIGS. 17A-17C depict orthogonal placement of diverse nanodevice components using CSMOP in one fabrication process. FIG. 17A shows a schematic in which pre-assembled NPs with different origami shapes separately with the same binding DNA sequence, followed by orthogonal placement onto lithography defined patterns of matching shapes. FIG. 17B shows an orthogonal placement of origami shapes each presenting unique DNA binding sequences onto lithography defined patterns of matching shapes, followed by hybridization of NPs functionalized with complementary DNA sequences to their corresponding origami shapes in one process. FIG. 17C shows multi-component devices can be achieved within each origami shape, whose complexity can be further enhanced with unique DNA barcodes for multiplexing.

DESCRIPTION

[0048] Nanofabrication can play a pivotal role in modem technology. Traditional top-down lithography, while effective in fabricating two dimensional (2D) patterns of tens of nanometers in size, encounters limitations in fidelity, efficiency, and scalability when fabricating sub- 10 nm features and three dimensional (3D) objects. [47-49] Bottom-up nanofabrication using DNA-based self-assembly has recently emerged as a scalable and environmentally benign approach that could in principle forego limitations of conventional nanofabrication. Structural DNA nanotechnology, especially the DNA origami method, has allowed us to program 3D nanostructures of virtually arbitrary shape and morphology with sub-nanometer scale precision. [50-57] Moreover, the advent of DNA origami techniques has provided a unique platform for the organization of molecules, [58- 60] proteins, [61-63] metallic nanoparticles (NPs), [21, 64-65] quantum dots (QDs) [29, 66-67] and other high-quality colloidal nanomaterials not accessible to lithography methods in precise and well-defined 3D configurations. [69-70] While this approach has created intricate, hierarchical, and hybrid nanodevices for various applications in biosensing, [70], therapeutics, [71], nanophotonics, [72], and more, the majority of them are limited to solution-dispersed structures up to a few hundred nanometers in size and lack coherence relative to each other. [0049] QDs are key candidates for quantum computing, quantum sensing, and quantum metrology through integrated quantum photonics [15, 16], One challenge to employ colloidal QDs in these devices is the need to accurately place and align controlled numbers and arrangements of QDs within nano- to micro- scale photonic circuits [17, 18], DNA nanotechnology, and in particular the DNA origami method, offers the unparalleled capability to program the position and orientation of nanomaterials at the nano- to micro- scale with sub-nanometer precision and intrinsic scalability using solution-based, bottom -up self-assembly [19-21], DNA origami-based nanomaterial integration into photonic devices represents one of the most promising routes towards this goal [22, 23],

[0050] One challenge limiting the programmability of QDs/QRs with DNA origami is the low conjugation yield of DNA ligands to their surfaces and their stability under aqueous buffer conditions required for DNA hybridization. As these semiconductor nanoparticles are generally synthesized in organic solvent with hydrophobic ligands, previously reported approaches first seek to transfer QDs and QRs dispersed in organic solvent to aqueous solution, which is often tedious and time consuming, before DNA can be conjugated to QDs and QRs via existing ligands or their cationic shell [24], Thiolated single-stranded DNA (ssDNA) is the most popular DNA derivative to functionalize the QD and QR surface [25], and previous approaches to conjugate it to QDs/QRs often require up to a few days [26-28], Moreover, the preceding approaches also suffer from limited numbers of functional single-stranded DNA (ssDNA) per QD and QR [26-28], which decreases the hybridization efficiency for complementary ssDNA and significantly affects the loading yield of QDs/QRs onto DNA origami structures [29], Recently, Ye et al develop the one- step ligand-exchange method to produce DNA conjugated QDs from organic solvent [28], however, it still requires several hours and the DNA number per QD did not increase compare with traditional salt-aged methods. Therefore, a fast and facile method for single-step preparation of QDs and QRs with high DNA ligand density directly from organic solvent can significantly lower the barrier for application of QD/QR materials using DNA nanostructures.

[0051] Another key challenge to manufacturing functional structures with DNA origami that can readily be incorporated into photonic devices is to transfer solution-synthesized origami- nanoparticle complexes to device substrates with controlled positioning and alignment, as well as maintaining structural fidelity and function in the dry state. Development of a new class of rigid 2D wireframe 6HB DNA structures [30, 31] can allow for the programming of arbitrary 2D DNA origami geometries with high structural fidelity, planarity, and rigidity, which can serve as robust templates to organize QDs/QRs on solid substrates. However, direct transfer of larger-scale soft materials such as DNA superstructures of these wireframe origamis [32] from solution to surface often suffers from aggregation and layered structures during the deposition and drying process. One promising method to circumvent this problem is to employ surface-assisted assembly, where building blocks bound to the surface of the substrate can diffuse freely in 3D and self-organize into defined arrangements. Self-assembly of DNA tiles [33] and origami structures [34-36] on lipid bilayer surfaces have been reported to form various 2D lattices, which, however, can collapse upon drying due to the soft nature of the lipid substrate. More importantly, long-range patterns of origamis on solid substrates have been demonstrated with the help of monovalent cations (Na⁺) to promote surface diffusion and organization [37-41], However, these examples only rely on either non-specific blunt-end interaction [37, 38] or merely surface crowding and shape matching to fit symmetrical origamis into 2D patterns [39-41], Lattice defects like grain boundary slipping can be observed frequently. More importantly, the anisotropic nature of the DNA sequences in the symmetrical origami shape is largely unaccounted for, leading to random orientations of a specific DNA duplex in each origami tile. Hence, these 2D patterns are not suitable to template other functional material into lattices.

[0052] Incorporating bottom-up DNA origami self-assembly with top-down 2D lithography can overcome the limitations of each approach towards scalable integrated hybrid nanodevices with single-nanometer resolution. Previously, lithography method has been employed to regulate the placement of large metal nanoparticles through DNA hybridization or capillary forces. [73-80], Pioneering works have developed the DNA origami placement (DOP) method where 2D [22, 81- 83] and 3D [84] DNA origami objects can be precisely positioned onto electron beam lithography (EBL) defined hydrophilic landing pads of matching shapes on a hydrophobically passivated silicon wafer substrate. Other efforts have explored various substrates [85-88] and lithography methods [89-91] for the controlled placement of DNA origami. In general, this method relies on origami in solution to bind the landing pad on the substrate, and further diffuse to fit the predefined landing pad shape to maximize binding energy. This process, however, can lead to kinetically trapped orientations with asymmetric origami shapes. Recently, a major development in the method has achieved absolute and arbitrary orientation control with a carefully designed asymmetric origami shape, whose landing pad binding energy landscape had a single minimum. [23] Yet, this impressive capability is limited to the specific origami design. A general method to tackle kinetically trapped states that applies to a variety of origami shapes is highly desired to enable the integration of diverse origami devices.

[0053] Quantum dots (QDs) are promising materials for a wide variety of applications in displays, lasers, sensors, solar energy conversion, quantum information, etc. Colloidal synthesis, a scalable method, is employed for producing high-quality QDs with tunable chemical, electrical, and optical characteristics for commercial use. Despite this, achieving individual deterministic and nanoscale placement accuracy of colloidally synthesized QDs on chip-based devices remains a challenge. This precision is particularly crucial for nanodevice applications in integrated photonic devices and quantum information science.

[0054] For example, functionalized colloidal QDs and quantum rods (QRs) with dense surface DNA ligands through a dehydration-assisted DNA conjugation method are promising candidates for these applications. We have demonstrated their precise hybridization onto DNA origami with nanometer-scale accuracy and orientation control. [67] By combining QD/QR hybridization with DNA origami and leveraging lithography-guided origami placement, the fabrication of state-of- the-art nanophotonic devices can be simplified and novel device structures can be accessed.

[0055] The method can include mixing an organic-phase of suspended nanoparticles with an aqueous phase of thiolated DNA including a cation such as Na⁺; allowing the mixture to emulsify, dehydrating the mixture by adding an alcohol such as 1 -butanol to collapse the DNA onto the nanoparticle (i.e. "dehydrate" it), and resuspending the mixture in aqueous buffer; and purifying the QDs via centrifugation.

[0056] In one aspect, a method of forming a DNA functionalized complex can include mixing thiolated DNA with a plurality of an inorganic moiety in an organic solvent to form a mixture; and dehydrating the mixture to form the DNA functionalized complex. The method can include recovering the DNA functionalized complex.

[0057] In certain embodiments, the array includes a wireframe DNA origami structure or assembly of multiple DNA origami structures. The wireframe DNA origami structure can include a crossover design or hybridization or base-stacking or other interfacial self-assembly design.

[0058] The inorganic moieties can be assembled to origami lattices with controlled positions, inter-particle distances and orientations. The positions and distances can be determined from the DNA sequence used to create the DNA origami structure. The DNA origami structure can create a two dimensional shape. The two dimensional shape can be rhombic, square, scalene triangle, isosceles triangle, equilateral triangle, rectangular, trapezoid, pentagonal, hexagonal, heptagonal, or octagonal. The two dimensional shape can have two fold symmetry, three fold symmetry, four fold symmetry, five fold symmetry, or six fold symmetry. In certain embodiments, the two dimensional shape can be asymmetric. A dimension of the shape can be 10 nm, 20 nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm, 80 nm, 90 nm, 100 nm, 110 nm, 120 nm, 130 nm, 140 nm, 150 nm, 160 nm, 170 nm, 180 nm, 190 nm, or 200 nm.

[0059] The inorganic moiety can be located in a controlled position on the DNA origami structure. When the DNA origami structure are patterned on a surface or self assembled on a surface, the resulting lattice creates an array in which the specific locations and distances between the inorganic moieties can be specifically controlled. The origami lattices with controlled positions can have a programmable and specified loading yield over 10%, over 20%, over 30%, over 40%, 50%, over 60%, over 70%, over 80%, or over 90%.

[0060] The controlled pattern self-assembles either randomly or due to electrostatic interactions or DNA hybridization interactions between the surface and an origami or other affinity reagent, or by steric or other non-specific interactions that induce face-up self-assembly. In certain embodiments, a substrate can be patterned using a mask material that is lithographically altered to create positions in which the DNA origami structures can interact with the substrate. The DNA origami structures can self-assemble into a 2D lattice face up. The mask can be polymethylmethacrylate or other polymeric mask material.

[0061] A method of forming a 2D nanoparticle array can include tiling a plurality of DNA functionalized inorganic moieties on a surface in a regular controlled pattern. Tiling can include assembling DNA functionalized inorganic moieties in a controlled orientation on the surface. The tiling can result in a periodic structure.

[0062] The origami placement yield with CSMOP primarily depends on the cavity size, origami concentration, solution cation and placement time. In general, larger cavity size, higher origami concentration, and ion concentration and longer placement time lead to overall higher origami binding yield. However, larger cavity size also leads to multiple origamis placed in the same cavity and broader origami orientation distributions.

[0063] In another aspect, a method of fabricating controlled arrays on a two dimensional solid surface can include preparing a substrate to include a pattern of shapes, and depositing a plurality of DNA origami structures in the pattern of shapes. The pattern of shapes can be formed with a mask material. For example, light or electron beam lithography can be used to create a pattern in the mask material on the substrate. The lithography can form shapes and patterns of shapes in the mask material. The method can include an exposed area of the shape on the substrate, for example, oxygen plasma etching which can enhance the binding of the origami structure to the surface of the substrate. The method can include removing the mask material after depositing the DNA origami structures. The method can also include exposing the deposited DNA origami structures in the pattern of shapes to a nanocrystal material having an affinity for the DNA origami structures. In certain circumstances, depositing the plurality of DNA origami structures in the pattern of shapes can include exposing the structures to a solution including a monovalent cation, such as sodium ion. This approach can improve the array quality. In certain embodiments, the plurality of DNA origami structures can have one or more geometries that match with one or more shapes of the pattern of shapes. [0064] In certain embodiments, a first step can include pre-assembly of various inorganic moi eties to different origami shapes separately with the same binding DNA sequence, followed by orthogonal placement onto lithography defined patterns of matching shapes that are patterned on a surface of a substrate. Alternatively, orthogonal placement of origami shapes can be achieved with each presenting unique DNA binding sequences onto lithography defined patterns of matching shapes, followed by hybridization of NPs functionalized with complementary DNA sequences to their corresponding origami shapes in one process. The orthogonal placement or shape placement can result in at least two different structures in the array. The multiplexity of the number of different structures can be two, three, four, five, six, seven, eight, nine, ten, or more based on different shapes or origami binding sequences. The identities of a mixture of DNA origami structures can be identified or tracked using a DNA reporter bar code tag, such as a fluorophore.

[0065] In certain embodiments, dehydrating the mixture includes adding an alcohol to the mixture. The alcohol can include a C1-C8 alcohol, for example, 1 -butanol.

[0066] In certain embodiments, the inorganic moiety includes a metal complex, a nanosphere, a nanorod, or other nanoshape. For example, the inorganic moiety includes a nanoparticle having a size of less than 50 nm, less than 40 nm, less than 30 nm, less than 20 nm, or less than 10 nm.

[0067] The array can include a monolayer of nanoparticle face-selecting overhangs.

[0068] In certain circumstances, the method can include annealing the array. This can improve the quality of the array by allowing the DNA origami structures to repair assembly defects. The presence of a single charge ion, such as sodium, can improve the quality of the annealed structure. The patterning or annealing can improve periodicity and orientation of the origami structures. For example, assembly in a patterned surface or annealing, or both, can result in highly ordered structure having less than 10%, less than 8%, less than 6%, less than 5%, or less than 4% deviation from a desired angle of orientation of origami structures or desired distance spacing between inorganic moieities. In certain circumstances, annealing the array can include thermally annealing either with or without mechanical or other vibration or shaking to enhance self-assembly kinetics and/or yield.

[0069] In another aspect, an array comprising a plurality of inorganic moieties can be aligned in a monolayer 2D array with a controlled spacing and orientation between each inorganic moieties arising from a DNA origami lattice on a substrate.

[0070] In another aspect, a superstructure of aligned semiconductor arrays can include:

1) a solid substrate surface;

2) a two-dimensional nucleic acid structure lattice; and

3) colloidal semiconductor nanocrystals bound to nucleic acid structures.

[0071] In certain circumstances, the two-dimensional nucleic acid structure lattice can be assembled directly on the solid substrate surface with the nucleic acid structure monomers.

[0072] In certain circumstances, the nucleic acid structure monomers within said lattice can present periodic and uniformly aligned binding nucleic acid overhangs extended away from said solid surface.

[0073] In certain circumstances, the colloidal semiconductor nanocrystals can bind to said nucleic acid structure lattice through nucleic acid hybridization and align locally by the shapematching arrangement of the overhangs on said nucleic acid structure monomers, if the semiconductor is anisotropic; and periodically by the repeating binding nucleic acid overhangs in each monomer in said lattice.

[0074] In certain circumstances, a DNA origami structure can have a wireframe planar shape with parallel edges where the edges are a 6-helix bundle structure of DNA, short crossover DNA overhangs with unique sequences extended in-plane from half of the edges wherein these edges are not parallel to each other, hybridization vacancies on the rest of the edges at the same corresponding locations wherein said crossover DNA overhangs on their parallel counterparts can hybridize to the vacancies, creating anti-parallel crossovers between tiles, short binding DNA overhangs extended out-of-plane to one side of the tile, wherein the overhang sequence is complementary to that of the DNA strands on a composite, and short face-selecting single stranded DNA overhangs extended out-of-plane to the same side of the tile as said binding DNA overhangs.

[0075] In certain embodiments, each overhang can be 2 base residues, 3 base residues, 4 base residues, 5 base residues, 6 base residues, 7 base residues, 8 base residues, 9 base residues, or 10 base residues.

[0076] In certain circumstances, a composite can include a QD/QR and a corona of closely packed DNA strands conjugated to its surface with a record high DNA loading density. For example, the composite can be stable in aqueous solution with a high salt concentration (e.g. IM sodium ion or 12.5mM magnesium ion). The composite can hybridize to DNA origami structures with higher efficiency than DNA functionalize QDs/QRs produced with other methods.

[0077] In certain embodiments, each of the inorganic moieties can be group II- VI (e.g. CdS, CdSe, CdTe, ZnS, ZnSe, ZnTe), group IV-VI (e.g. PbS, PbSe), group III-V (e.g., InP, GaAs), group I- VI (e.g. Ag2S, A 2Se, Ag2Te) or group I-III-VI (e.g. AglnS, AglnSe, CuInS, CuInSe), or their core-shell structured composites. For example, each of the inorganic moieties can be a nanoparticles including gold, InP, CdSe, CdTe, CdS, ZnS, ZnSe, Ag2Te, Ag Se, Ag2S, PbS, PbSe, CdSe/CdS core/shell, CdSe/ZnS core/shell, ZnSe/ZnS core/shell, alloyed CdSeS, alloyed CdSeTe, or alloyed CdZnSe.

[0078] In another aspect and example, a method for fabricating aligned colloidal semiconductor nanocrystal arrays on a two dimensional (2D) solid surface can include surface- assisted large scale assembly of components. The aligned colloidal semiconductor nanocrystal arrays can be periodic in 2D space, and if the colloidal semiconductor nanocrystal is anisotropic in shape (i.e. non-spherical), its orientation is aligned with its periodic replicates across the 2D space. The periodicity can be 20 nm, 30 nm, 40 nm, 50 nm, 60 nm, 70 nm or 80 nm spacing.

[0079] In certain circumstances, the colloidal semiconductor nanocrystal arrays can be infinite across a 2D surface or finite as size and shape defined regions on a surface.

[0080] In certain circumstances, the colloidal semiconductor nanocrystals are aligned using nucleic acid structures as a template, wherein the colloidal semiconductor nanocrystal attaches to a nucleic acid structure monomer at a specific location, and if the colloidal semiconductor nanocrystal is anisotropic in shape (i.e. non-spherical), it binds to the nucleic acid structure with a pre-defined orientation.

[0081] In certain embodiments, the nucleic acid structure template can be aligned in an array by assembling into a 2D lattice superstructure on a surface; and/or attaching to location and orientation prescribed shape-matching landing pads on a surface.

[0082] In certain embodiments, nucleic acid structure array can contain one or more unique nucleic acid structure geometries. Each nucleic acid structure geometry templates one or more types of colloidal semiconductor nanocrystals with one or more pre-defined orientations. The nucleic acid structure can be a wireframe DNA origami.

[0083] In certain embodiments, the colloidal semiconductor nanocrystal is a quantum dot (QD) or a quantum rod (QR).

[0084] In other embodiments, a method for fabricating QD and QR 2D arrays with a nucleic acid structure 2D lattice can include the steps of:

1) functionalizing QDs and QRs with a dense layer of DNA sequence, wherein the QDs and QRs are functionalized and phase-transferred in a single step and remain stable;

2) fabricating 2D DNA origami lattice templates on surface, wherein the origami units in the lattice present uniformly addressable binding sites for DNA hybridization; and

3) assembling DNA-functionalized QDs and QRs to the origami lattice template via DNA hybridization, wherein the QDs and QRs are aligned in space and orientation.

[0085] In certain circumstances, step 1) can be accomplished by an ultrafast dehydration- assisted DNA conjugation method comprising the steps of:

1) mixing QDs/QRs dispersed in organic solvent with thiol -derivatized DNA in aqueous solution and sodium salt solution;

2) ultrasonicating the mixture until emulsion is observed;

3) adding a C1-C8 alcohol (for example, 1 -butanol) to dehydrate the mixture; and

4) adding aqueous buffer to rehydrate and recover the DNA functionalized QDs/QRs.

[0086] In certain embodiments, the QDs/QRs dispersed in organic solvent in step 1) can be any semiconductor nanocrystals of group II- VI (e.g. CdS, CdSe, CdTe, ZnS, ZnSe, ZnTe), group IV-VI (e.g. PbS, PbSe), group III-V (e.g, InP, GaAs), group I- VI (e.g. Ag2S, Ag2Se, Ag2Te) or group I-III-VI e.g. AglnS, AglnSe, CuInS, CuInSe), or their core-shell structured composites, capped with trioctylphosphine oxide (TOPO), octadecyl amine, or oleic acid ligand, and/or dispersed in common organic solvents (e.g. hexane, toluene, chloroform).

[0087] In certain embodiments, the thiol-derivatized DNA in step 1) can be single stranded or double stranded oligo nucleic acids of any sequence with one or greater number of thiol functional groups conjugated to either the 5’ or the 3’ terminal of the nucleic acid molecule.

[0088] In certain embodiments, the final sodium salt concentration in step 1) can be 50nM, 60mM, 70mM, 80mM, 90mM or lOOmM regarding to the sodium ion.

[0089] In certain embodiments, the molar ratio of thiol-derivatized DNA to QDs/QRs in step 1) can be greater than 0.8 (/nm²) x the surface area (nm²) of the QD/QR used.

[0090] In certain embodiments, the ultrasonication in step 2) can take about 1 min, about 2 min, about 3 min, about 4 min, about 5 min, about 6 min, about 7 min, or about 8 min in an ultrasonicator.

[0091] In certain embodiments, the volume of 1-butanol added in step 3) is more than 2 times, more than 3 times, more than 4 times, more than 5 times, more than 6 times, more than 10 times, more than 12 times, more than 15 times or more than 20 times the final volume of the mixture in step 1).

[0092] In certain embodiments, the aqueous buffer added in step 4) can an alkaline buffer with a pH of 7-9.

[0093] In certain embodiments, the volume of the aqueous buffer added in step 4) can be less than the volume of the 1-butanol added step 3), for example, about 1/3 the volume. [0094] In certain embodiments, the QDs/QRs are functionalized with DNA strands and phase- transferred from organic solvents to aqueous solutions with a total processing time less than 20 min.

[0095] In certain embodiments, step 2) can be accomplished by a Surface- Assisted Large- Scale Assembly (SALSA) method comprising the steps of:

1) folding DNA origami tiles, wherein the tiles possess lateral in-plane affinity to each other;

2) mixing said tiles with NaCl solution;

3) incubating said mixture in contact with a solid surface while annealing thermally; and

4) washing the solid surface to remove unbound substances.

[0096] In certain embodiments, the final concentration of the origami tile is 500pM and the final concentration of NaCl is 0.5M in step 2).

[0097] In certain embodiments, the solid surface in step 3) can be a freshly cleaved mica surface or a silicon surface.

[0098] In certain embodiments, the thermal annealing in step 3) can be performed on a hotplate shaker with 12 cycles of consecutive heating at 60°C, 55°C, 50°C for 1 hr each (36 hr in total) with 200 rpm shaking, and then letting the setup cool down to room temperature undisturbed.

[0099] In certain embodiments, the washing can be accomplished by rinsing the mica surface with lOOpL buffer dropwise for 5, 8, 10, 12 or 16 times.

[00100] In certain embodiments, step 3) can be accomplished by incubating the composite with a washed mica surface for over 4 hrs. [00101] In certain embodiments, the method can include washing the incubated mica surface with lOOpL buffer dropwise for 16 times, incubating the surface with lOmM NiCh solution for lOmin, washing the surface 3 times with lOOpL, and drying with a flow of compressed air.

[00102] In certain embodiments, a method for fabricating QD and QR 2D arrays with prescribed landing pads on surface can include the steps of:

1) prescribing location and orientation prescribed shape-matching landing pads on surface;

2) attaching said DNA origami structure of claim 44 to said landing pads; and

3) assembling said composite of claim 40 to said DNA origami structure attached to the landing pads.

[00103] In certain embodiments, step 1) can be accomplished by prescribing DNA-binding landing pads via lithography methods, wherein the landing pads are of various sizes and shapes.

[00104] In certain embodiments, step 2) can be accomplished by attaching one or more DNA origami structures of matching sizes and shapes to said landing pads, wherein an annealing process is employed to attach more than one class of origamis with different shapes to their corresponding landing pads in the same process orthogonally, via shape-matching.

[00105] In certain embodiments, step 3) can be accomplished by assembling one or more types of DNA-functionalized QDs/QRs to said DNA origami structures on said landing pads presenting complementary DNA sequences.

[00106] Unexpectedly, Na⁺ mediated surface-assisted large-scale assembly is improved, in part because the monovalent cation promotes the diffusion and assembly of origami tiles. Also, thermal annealing to break misassembled origami tiles for error correction. Moreover the methods described herein can control which side of the origami lands on the substrate. Na⁺ mediates the binding affinity and possibly the elevated temperature promoting dynamics, this method was able to bias the non-binding face of the origami landing on a mica surface.

[00107] It was also unexpected that increasing EBL dose impacts long axis angle distribution, meaning longer exposures increased dispersity of orientation. For example, orientation can be controlled along a long axis of the origami structure to be within 20 degrees, within 15 degrees, within 10 degrees or within 5 degrees of a selected angle.

Dehydration-assisted DNA conjugation to QDs/QRs

[00108] Ultrafast preparation of high-density DNA functionalization of QDs and QRs can use a dehydration-assisted phase transfer method, as illustrated in FIG. 1. QDs or QRs dispersed in organic solvent were incubated with thiol-derivatized ssDNA and Na⁺, followed with sonication until the observation of emulsion. Then 1 -butanol was added for the dehydration of the mixture, which can condense ssDNA onto the surface of QDs and QRs for efficient conjugation. Finally, aqueous buffer was added to rehydrate and recover the QDs/QRs-DNA produced by dehydration- assisted conjugation (dQDs/dQRs) with high-density surface DNA. In a typical experiment, thiolated ssDNA (5’-thiol-AAAAAAAAACCCAGGTTGCTCT-3’ (SEQ ID NO. 1)) was added to octadecylamine or oleic acid capped QDs/QRs at a desired molar ratio (200: 1 for QDs with fluorescence emission at 600 nm (QD600); 500:1 for QD660; 200:1 for QR560; 500:1 for QR620) in the presence of 100 mM Na⁺ to reach a final volume of 50 pL. Such solution was sonicated around 5 min, and then immediately combined with 600 pL 1 -butanol followed by a quick vortex for several seconds. Subsequently, 200 pL of 0.5 x TBE (Tris, 44.5 mM; EDTA, 1 mM; boric acid, 44.5 mM; pH 8.0) buffer was added to the above solution followed by another quick vortex and a brief centrifugation at 2000 g for several seconds to facilitate a liquid phase separation. DNA- functionalized QDs/QRs were then recovered as a sublayer of the resulting two immiscible liquids. To remove excess ssDNA, DNA-functionalized QDs/QRs were purified and concentrated using an ultracentrifugal filter (Amicon 100 kDa) five times at 8,000 g for 3 min for each centrifugation step. The whole process was carried out under ambient conditions, assisted only by sonication, vortex mixing and centrifugation-facilitated phase separation. The time required from solution mixing to product recovery was as short as 20 minutes.

[00109] To quantify DNA density per dQD/dQR, 5’-thiolated DNA with an extra fluorescent modifier (FAM) at the 3’ terminus (sequence: 5 ’-thiol - AAAAAAAAACCCAGGTTGCTCT-FAM-3’ (SEQ ID NO. 1)) was used to prepare dQD/dQR. The concentrations of QDs/QRs were obtained by UV-vis extinction spectroscopy with diameterdependent extinction coefficients calculated from an empirical equation [42, 43], Correspondingly, the following extinction coefficients at 350 nm were used for determining the molar concentrations of 6 nm QD, 14 nm QD, 4/16 nm (diameter/length) QR, and 5/29 nm QR: 3.0* 10⁶ M'¹ cm'¹, 2.9* 10⁷ M'¹ cm'¹, 2.3 x lO⁷ M'¹ cm'¹, and 6.4* 10⁷ M'¹ cm'¹. And the actual sizes of the QDs and QRs were measured by TEM (FIG. 2A). DNA concentration was determined by FAM fluorescence calibration curve (FIGS. 2B and 2C). Fluorescence was excited at 485 nm with emission recorded from 500 to 700 nm, and dQDs/dQRs prepared in three parallel batches to give an averaged DNA density. The ssDNA number per dQD600, dQD660, dQR560, and dQR620 were 21, 135, 42, and 105, respectively (FIG. 2D). For comparison, DNA-functionalized QD/QR (mQD/mQR) were also prepared by a method as described previously [26, 27, 44], The ssDNA number per mQD600, mQD660, mQR560, and mQR620 were 3, 9, 6, and 12, respectively (FIG. 2D).

[00110] Two key factors can be considered to prepare high-density DNA functionalization of QDs and QRs: Na⁺ and 1-butanol/water volume ratio. Here agarose gel electrophoresis (AGE) was used to precheck DNA (51 nt) loadings on QD660 based on increased gel retardation. As shown in FIG. 3 A, dQD660 was prepared using thiolated DNA (Case 1), or combined with NaOH (Case 2), or NaOH and trioctylphosphine oxide (TOPO) (Case 3), or NaOH and tetrabutylammonium bromide (TBAB) (Case 4), or NaOH, TOPO, and TBAB (Case 5). It should be noted that NaOH was only used to compare with traditional TOPO and TBAB methods involving QD/QR phase transfer steps. The NaCl can also work for dehydration-assisted phase transfer method. The AGE gel image showed the DNA density per QD660 was significantly increased due to the presence of NaOH. In a typical experiment, for above Case 1, 20 pL of thiolated ssDNA was added to 5 pL of octadecylamine capped QD660 at a molar ratio of 500: 1 to reach a final volume of 50 pL. For above Case 2, 20 pL of thiolated ssDNA was added to 5 pL of octadecylamine capped QD660 at a molar ratio of 500: 1 in the presence of 100 mM NaOH to reach a final volume of 50 pL. For above Case 3, 5 pL of octadecylamine capped QD660 was incubated with 5 pL of TOPO (1 g/ 10 mL) for 30 minutes, 20 pL of thiolated ssDNA was added to above mixture at a molar ratio of 500: 1 in the presence of 100 mM NaOH to reach a final volume of 50 pL. For above Case 4, 5 pL of octadecylamine capped QD660 was incubated with 2 pL of TBAB (0.3 M) for 30 minutes, 20 pL of thiolated ssDNA was added to above mixture at a molar ratio of 500: 1 in the presence of 100 mM NaOH to reach a final volume of 50 pL. For above Case 5, 5 pL of octadecylamine capped QD660 was incubated with 5 pL of TOPO (1 g/ 10 mL) and 2 pL of TBAB (0.3 M) for 30 minutes, 20 pL of thiolated ssDNA was added to above mixture at a molar ratio of 500: 1 in the presence of 100 mM NaOH to reach a final volume of 50 pL. Such solution was sonicated around 5 min, and then was immediately combined with 600 pL 1 -butanol followed by a quick vortex for several seconds. Subsequently, 200 pL of 0.5 x TBE buffer was added to the above solution followed by another quick vortex and a brief centrifugation at 2000 g for several seconds to facilitate a liquid phase separation. DNA-functionalized QD660 were then recovered as a sublayer of the resulting two immiscible liquids. DNA-functionalized QD660 sample without purification (15 pL) was combined with 3 pL of 6* loading buffer (NEB) and loaded to a 1% agarose gel with 0.5* TBE. Each gel was run at 65 V for 60 min in 0.5 x TBE at 4 °C. Gels were then visualized under blue light transilluminator.

[00111] Moreover, different 1 -butanol/water ratio was used to prepare the dQD660, as shown in FIG. 3B, a 1 -butanol/water ratio of 12: 1 could lead to the highest DNA density per QD660. In a typical experiment, thiolated ssDNA was added to octadecylamine capped QD660 at a molar ratio of 500: 1 in the presence of 100 mM Na⁺ to reach a final volume of 50 pL. Such solution was sonicated around 5 min, and then was immediately combined with 50, 300, 450, 600, or 750 pL 1 -butanol followed by a quick vortex for several seconds. Subsequently, 20, 100, 150, 200, or 250 pL of 0.5 x TBE buffer was added to the above solution followed by another quick vortex and a brief centrifugation at 2000 g for several seconds to facilitate a liquid phase separation. DNA-functionalized QD660 were then recovered as a sublayer of the resulting two immiscible liquids. DNA-functionalized QD660 sample without purification (15 pL) was combined with 3 pL of 6* loading buffer (NEB) and loaded to a 1% agarose gel with 0.5* TBE. Each gel was run at 65 V for 60 min in 0.5* TBE at 4 °C. Gels were then visualized under blue light transilluminator.

[00112] Furthermore, various dehydration time was tested for dQD660 preparation. AGE image showed the dQD660 was formed immediately during dehydration. Prolonged aging under dehydration was not needed (FIG. 3C). In a typical experiment, thiolated ssDNA (51 nt) was added to octadecylamine capped QD660 at a molar ratio of 500: 1 in the presence of 100 mM Na⁺ to reach a final volume of 50 pL. Such solution was sonicated around 5 min, and then was immediately combined with 600 pL 1 -butanol followed by a quick vortex for several seconds. After 0, 30, 60, or 90 min incubation and shaking, 200 pL of 0.5 x TBE buffer was added to the above solution followed by another quick vortex and a brief centrifugation at 2000 g for several seconds to facilitate a liquid phase separation. DNA-functionalized QD660 were then recovered as a sublayer of the resulting two immiscible liquids. DNA-functionalized QD660 sample without purification (15 pL) was combined with 3 pL of 6x loading buffer (NEB) and loaded to a 1% agarose gel with 0.5* TBE. Each gel was run at 65 V for 60 min in 0.5* TBE at 4 °C. Gels were then visualized under blue light transilluminator.

[00113] InP/ZnS QDs are widely utilized QLED displays due to their cadmium-free composition. [46] The absence of cadmium in these QDs enhances their environmental friendliness compared to traditional CdSe/ZnS QDs. In another example, the ultrafast preparation of high- density DNA functionalization of InP/ZnS QDs was demonstrated using a dehydration-assisted phase transfer method. InP/ZnS QDs dispersed in organic solvent were incubated with thiol- derivatized ssDNA, Na⁺, and tris(2-carboxyethyl)phosphine (TCEP), followed with sonication until the observation of emulsion. Then 1 -butanol was added for the dehydration of the mixture, which can condense ssDNA onto the surface of InP/ZnS QDs for efficient conjugation. Finally, aqueous buffer was added to rehydrate and recover the InP/ZnS QDs-DNA produced by dehydration-assisted conjugation (dQDs) with high-density surface DNA (FIGS. 10A-10C). In a typical experiment, thiolated ssDNA (sequence: 5’-thiol-AAAAAAAAACCCAGGTTGCTCT-3’ (SEQ ID NO. 1)) was added to oleic acid capped InP/ZnS QD (emission at 530, 590, 620, and 650 nm) at a desired molar ratio (500: 1) in the presence of 100 mM NaOH and 50 mM TCEP to reach a final volume of 50 pL. Such solution was sonicated around 5 min, and then immediately combined with 600 pL 1 -butanol followed by a quick vortex for several seconds. Subsequently, 200 pL of 0.5 x TBE (Tris, 44.5 mM; EDTA, 1 mM; boric acid, 44.5 mM; pH 8.0) buffer was added to the above solution followed by another quick vortex and a brief centrifugation at 2000 g for several seconds to facilitate a liquid phase separation. DNA-functionalized InP/ZnS QDs were then recovered as a sublayer of the resulting two immiscible liquids. To remove excess ssDNA, DNA-functionalized InP/ZnS QDs were purified and concentrated using an ultracentrifugal filter (Amicon 100 kDa) five times at 8,000 g for 3 min for each centrifugation step.

Hybridization ability and loading efficiency of QD/QR-DNA origami assemblies

[00114] The high-density of DNA ligands on these QDs/QRs endows them with excellent stability in aqueous solution with various salt and buffer conditions and enables their fast binding onto DNA origami structures with high binding yield and nanometer-scale placement precision. To emphasize the hybridization ability of dQD and dQR, 10 nM of dQD600, dQD660, dQR560, and dQR620 was incubated with a complementary ssDNA with a fluorescent modifier (Cy5, Cyanine5) at the 3’ terminus (sequence: 5’-AGAGAACCTGGG-Cy5-3’ (SEQ ID NO. 2)) at a desired molar ratio (1 :200 for QD600 and QR560;l :500 for QD660 and QR620) in l x PBS to reach a final volume of 50 pL (FIG. 4A). For comparison, mQD600, mQD660, mQR560, and mQR620 were also incubated with a complementary ssDNA labeled with Cy5 at the same condition (FIG. 4A). The conjugated dye on the complementary ssDNA provides a distinct measurable signal in the absorbance and emission spectra of the QD/QR-dye hybrids (FIG. 4B), which were used to quantify the FRET efficiency with steady-state measurements. After 2-hour incubation, the fluorescence emission spectra of QDs/QRs alone and in the presence of Cy5 were recorded (FIGS. 4D-4G). The fluorescence was excited at 450 nm with its emission being recorded from 500 to 800 nm, and all samples prepared in three parallel batches were employed to give an averaged FRET efficiency. Compared with the mQD/mQR-Cy5 FRET, FRET efficiency of dQD/dQR-Cy5 FRET pairs calculated from steady-state measurement increased from 63 ± 4% to 83 ± 1%, from 36 ± 1% to 88 ± 1%, from 38 ± 1% to 62 ± 5%, and from 45± 4% to 87 ± 3% for QD600-Cy5, QD660 -Cy5, QR560-Cy5, and QR620-Cy5, respectively, indicating the increasing number of dye acceptors due to high-density DNA functionalization on QDs/QRs surface (FIG. 4C).

[00115] Having demonstrated the highly efficient hybridization ability of dQD and dQR, the loading efficiency of QD/QR-DNA origami assemblies was tested. 40 nM of dQR620, mQR620, dQD660, and mQD660 were incubated with 10 nM 6HB wireframe rhombic origami in l x TAE with 12 mM MgChto reach a final volume of 50 pL, respectively. After overnight incubation, 10 pL of QD/QR-DNA origami assemblies were adsorbed on glow-discharged 400 mesh carbon film square grids and stained by 2% aqueous uranyl formate solution containing 25 mM of NaOH. The structural characterization of QD/QR- DNA origami assemblies were carried out using a ThermoFisher FEI Tecnai Spirit Transmission Electron Microscopy operating at 120 kV. As shown in FIG. 5, dQR620 can be aligned along 6HB edges with high fidelity (86%) which is a significant improvement comparing to mQR620 prepared via traditional phase-transfer and conjugation method (14%). A high proportion of di-valent dQD660 assemblies were noticed that could still form even when rhombic origami was incubated with four-fold excess dQD660, which could be explained by the highly efficient hybridization ability of dQD660, the high-density ssDNA binding sites on dQD660 can still bind other DNA origami after formation of QD-DNA origami assemblies.

Surf ace- Assisted Large-Scale Assembly (SAESA) and aligned QR 2D lattice fabrication

[00116] SALSA with a rigid 6HB wireframe rhombic origami designed by ATHENA [45], an open-source Graphical User Interface (GUI) software for automated sequence design of 2D and 3D wireframe scaffolded DNA origami, was demonstrated. The key to achieve full orientation control of origami tiles within a 2D lattices is to introduce anisotropic lateral interactions between neighboring origamis. This was realized by introducing DNA overhangs that can hybridize to a specific vacancy on the adjacent origami. As shown in FIG. 6A, two neighboring edges of the origami are each designed with 2 crossover strands (solid circles and squares) with unique sequences that are complementary to their parallel counterparts with 2 hybridization vacancies (hollow circles and squares). Although there are two modes for the tiling of a rhombic geometry, hexagonal and orthorhombic, the 2D lattice can only be thermodynamically stable when the designed crossovers hybridize to their corresponding vacancies, directing the formation of the hexagonal lattice specifically. The inter-tile binding affinity can be tuned by the length of the crossover overhang sequence. An 8-nucleotide (8nt) overhang design can have limited origami self-assembly in solution at room temperature but enables 2D lattice assembly through SALSA. The assembly of this extended hexagonal lattice can be carried out in solution through thermal annealing (FIG. 6B), which, however, often results in layered structures or random aggregations during the sample deposition (here by dropcast) and drying step, as shown in FIG. 6C.

[00117] Hence, a surfaces-assisted method was employed to directly assemble 2D lattices of the rhombic origami tiles with lateral crossovers and full orientation control on mica surface. Monovalent cation (sodium) was used to tune the electrostatic interaction between the origami and the negatively charged substrate to allow the on-surface diffusion of origami monomers and their coalescence when the lateral anti-parallel crossovers match to generate a hexagonal lattice. Specifically, the 6HB wireframe rhombic origami was first produced using a reported method [32] in a Tris (tris(hydroxymethyl)aminomethane) buffer containing 40 mM Tris and 12.5 mM MgCh with a pH adjusted to 8.3 ± 0.2 (1 *TMg). In a typical SALSA process, the as synthesized origami was mixed with a concentrated NaCl solution (5 M) for a 1.5 mL solution with a final origami concentration of 500 pM and a Na⁺ concentration of 0.5 M. This mixture was added to a well on a 48-well microplate and a freshly cleaved mica disc (D = 12 mm) was placed on top of the liquid surface in the well, floating with the cleaved side in contact with the solution surface. Then the microplate was sealed and placed on a hotplate shaker (BioShake iQ, QInstruments) for 12 cycles of heating at 60°C, 55°C, 50°C for 1 hr each (36 hr in total) with 200 rpm shaking, and then let the setup naturally cool down to room temperature. The mica disc was then taken out of the microplate well and carefully rinsed with 100 pL l *TMg buffer (with 0.5M Na⁺) 10 times, with l *TMg buffer (without Na⁺) 6 times and with 1 *TNi (40 mM Tris and 12.5 mM MgCI with a pH adjusted to 8.3 ± 0.2) 3 times before incubating with 50 pL l*TNi on the disc for 5-10 min. After the incubation, the disc was rinsed with 100 pL Milli-Q water 3 times and dried with compressed air. Next, the mica disc was kept under vacuum for at least Ihr prior to AFM imaging.

[00118] Three synergistic effects are key to the formation of large origami lattices were discovered: 1) Na⁺ mediated surface-assisted large-scale assembly where the monovalent cation promotes the diffusion and assembly of origami tiles; 2) thermal annealing to break mis-assembled origami tiles for error correction; and 3) the control of which side of the origami lands on the substrate. Without or with a low concentration (< 100 nM) of the Na⁺, the affinity of the origami to the mica surface is so strong that the origami tiles cannot move to form ordered lattices once they attach to the surface. Without thermal annealing, only small 2D arrays were observed due to mis-assembled origami tiles. Heating at a higher temperature (> 60 °C) can start to denature DNA origami and lower the surface coverage. Longer annealing time (12 cycles instead of 5 cycles) also help produce large 2D origami lattices to some extent. It was found that the conditions above yield the best 2D lattice so far.

[00119] Another key factor to fabricate large 2D origami lattices is to ensure that all origami tiles landed on the substrate with the same side. As shown in FIG. 7A, five QR binding strands (red) were introduced along the long axis of the wireframe rhombic origami, whose side was denoted as the upside or the binding face. When depositing solution-based 2D origami structures onto a substrate, both the upside (grey) and the downside (cyan) can land on the surface, exposing or hiding the binding strand for QR respectively (FIG. 7B). Apart from the fact that the binding strands needs to be exposed for the subsequent functional material binding to the origami, origami tiles with different side landed on the surface cannot form 2D lattices together due to the fully anisotropic crossover design, limiting the growth of the 2D lattices to relatively small sizes (FIG. 7C). This challenge was tackled by introducing 31 additional face-selecting 20nt ssDNA overhangs (20 thymidine, green) to the binding face (FIG. 7D), which act as entropic brushes that interfere with origami binding to the substrate. It is worth to note that the ssDNA entropic brush method was previously believed to be ineffective to bias selected origami face binding to mica due to the strong DNA-mica affinity [23], However, it was discovered that with Na⁺ mediating the binding affinity and possibly the elevated temperature promoting dynamics, this method was able to bias the non-binding face of the origami landing on the mica surface (FIG. 7E). As a result, larger 2D lattices of origami tiles with all binding-face up can be fabricated on surface directly through SALSA (FIG. 7F).

[00120] To fabricate aligned QR lattices, dehydration enabled high DNA density QRs (dQR) to the pre-formed 2D origami lattices on surface were assembled (FIG. 8A). Specifically, during the preparation of the SALSA lattice, after lOx washing with 1 xTMg buffer (with 0.5M Na⁺), the mica disc was placed on the liquid surface of 600 pL dQR solution (1 nM dQR in l *TMg buffer with 0.5M Na⁺) in another well of the microplate. The setup was incubated at room temperature with 200 rpm shaking for 4 hrs or longer for QR binding. Next, the sample was transferred from the dQR solution to the liquid surface of a fresh 1 *TMg buffer (with 0.5M Na⁺) in another well of the microplate, heated at 50 °C for 2hrs and cooled down to room temperature naturally to remove excess dQRs. The sample was then carefully rinsed with 100 pL l *TMg buffer (without Na⁺) 6 times and with 1 xTNi 3 times before incubating with 50 pL 1 xTNi on the disc for 5-10 min. After the incubation, the disc was rinsed with 100 pL Milli-Q water 3 times and dried with compressed air. AFM images of as-synthesized aligned dQR lattice are shown in FIGS. 8B and 8C. The orientation analysis from AFM images showed that up to 73% of QRs were distributed within 30° for 2D lattice within a 1 pm² area, respectively. In contrast, QRs attached to 2D origami templates without crossovers (FIG. 8A) distributed randomly in orientation on the substrate (FIGS. 8D and 8E).

[00121] Furthermore, undergoing efforts are focused on prescribing location and orientation controlled shape-matching landing pads across a millimeter scale silicon chip substrate with lithographic methods for the binding of origami structures. One or more DNA origami structures of matching sizes and shapes can bind to their corresponding landing pads on the chip via shapematching affinity interactions, and 2D origami lattices can be grown from these bond origami seeds. QDs/QRs and other functional materials can then be aligned and arranged on these lattices with controlled spacing and orientation. This can allow device-ready fabrication of 2D QD/QR arrays on silicon chips.

[00122] In summary, Quantum dots (QDs) and quantum rods (QRs) have attracted extensive interest in next-generation display systems due to their bright and tunable narrowband photoluminescence (PL), especially in the field of micro-light-emitting-diode (p-LED) devices. Moreover, QDs are also key candidates for quantum computing, quantum sensing, and quantum metrology through integrated quantum photonics [15], Scalable fabrication of QD/QR arrays possessing controlled spacing and orientation with nanometer precision on a device substrate is essential to the advancement of such research and applications. DNA origami technology has offered a scalable bottom-up strategy to organize nanoparticles at the nanoscale with unparalleled programmability and versatility. However, multiplexing QDs and QRs with DNA origami structures has been challenging, primarily due to the low DNA conjugation density to QDs/QRs from existing methods, which often leads to poor colloidal stability and low binding efficiency. Here, an ultrafast strategy was developed to prepare high-density DNA functionalized QDs/QRs (0.17-0.21 DNA per nm²) directly from their organic solution using a dehydration and rehydration process that reduces the fabrication time from hours to a few minutes. As prepared QDs/QRs were stable in a range of salted buffer conditions and hybridize to DNA origami structures with excellent efficiency. To build device-ready QD/QR arrays, a Surface- Assisted Large-Scale Assembly (SALSA) method was further developed to construct 2D origami lattices directly on a solid substrate for QD/QR templating, which circumvents problems in transferring solution-assembled soft 2D materials to a device surface. A 6-helix-bundle (6HB) wireframe origami structure was designed by ATHENA, with high structural fidelity, planarity, and rigidity [32, 45], With unique anisotropic crossover designs between neighboring origami structures, 2D origami lattices up to micrometer scale are produced with the rational manipulation of surface diffusion, error correction and face selection. QDs and QRs were then assembled to the origami lattices with precisely controlled positions, inter-particle distances and orientations, with a loading yield over 90%. A monolayer QR array with aligned QR orientations was fabricated, which can function as a polarized light source due to the PL emission anisotropy along the long axis of QRs and their alignment on surface. These approaches can enable scalable fabrication of DNA-programmed QD and QR devices with nanoscale orientation and positioning accuracy for advanced applications in display, sensing and photonics.

Lithography guided DNA origami placement for quantum dot and quantum rod integration on silicon chips

[00123] Another approach to building device structures can include employing a Cavity-Shape Modulated Origami Placement (CSMOP) method to engineer the diffusion and binding kinetics of DNA origamis onto lithographically defined substrates, to facilitate precise orientation control of diverse origami shapes. Six helix bundle (6HB) wireframe origami structures were employed for their excellent planarity and rigidity, [30-31, 92] along with a reduced surface area that could interact with landing pads, conducive to dynamic binding. EBL was first utilized to define cavities of matching size and shape of the DNA origami on a silicon wafer substrate, where the bottom of the cavity was hydrophilic, and the sidewalls were hydrophobic. The cavity walls effectively prevented mis-oriented origami from binding to the bottom of the cavities with more than one edge of the shape, promoting diffusion and orientation correction. The electrostatic interaction of origami binding was further modulated with monovalent cation to achieve accurate orientation control over origami placement in high yield. The cavity shape can be used to modulate the origami that can be placed inside at a specific chip location, leading to the orthogonal placement of diverse individually addressable origami devices. To demonstrate the capability of the CSMOP method in nanofabrication, gold nanorods (AuNRs) were successfully assembled aligned to EBL-guided origamis on a silicon chip, presenting programmable orientation-dependent plasmonic light scattering. QDs and QRs were incorporated to the CSMOP method to fabricate photonic devices with location and orientation controlled QD/QR as quantum light sources for lasing, quantum sensing, and quantum computing.

[00124] The CSMOP method starts with defining cavities of the same shape as the origami structure on the silicon substrate with a 90 nm thick thermally grown silica (SiCh) layer (FIG. HA, step i) that can bind DNA origamis through magnesium ion (Mg²⁺) mediated electrostatic interaction. [81, 93-94] Building on prior methods [22, 81-82], the silica surface was passivated with trimethyl silyl (TMS) groups and spin coated the substrate with a hydrophobic polymethyl methacrylate (PMMA) resist layer typically ca. 60 nm in thickness, followed by defining cavities in the resist layer through electron beam lithography (EBL) and resist development. Oxygen plasma etching then converted the TMS coating at the bottom of the cavity to a silica surface presenting affinity to DNA origami (FIG. 11 A, step v). The physical topology constraints offered by the non-binding PMMA cavity shape can prevent mis-oriented origamis or origamis of a different shape from binding to the bottom silica surface strongly as they could only slide into the cavity with an edge of the DNA structure interacting with the bottom surface. DNA origami rigidity is essential to this mechanism as origami bending and deformation can increase the interacting surface area towards the cavity bottom surface. 6HB wireframe origami structures have demonstrated excellent planarity and rigidity, [30-31, 92] along with a reduced 2D surface area that interacts with a surface, conducive to dynamic binding. A rhombic 6HB wireframe origami with one side modified with single-stranded DNA (ssDNA) overhangs to prevent binding to the surface while offering handles (red) for subsequent nanomaterial templating was tested (FIG. 1 IB). [23, 67], This rhombic origami has a long diagonal axis of ca. 120 nm and a short diagonal axis of ca. 70 nm, with a two-fold rotational symmetry.

[00125] As described above, Arrays of rhombic cavities (250 nm apart) of varied sizes (see below) with a matched shape as the rhombic origami (FIG. 11C) on a 0.5 cm x 1 cm silicon chip were fabricated. The rhombic origami was folded at 1 nM with 12.5 mM Mg²⁺ and used without the need for purification, as excess staple strands did not affect the placement. A 20 pL solution of 500 pM origami containing 36 mM Mg²⁺ was then dropped on top of the cavity array and incubated at room temperature for 1 hr. After a simplified washing step, the chip was dried with a stream of compressed air. As shown in FIG. l id (and FIGS. 12A-12C), the origamis were located at the bottom of the PMMA cavities with orientations aligned to the cavity. No origamis were observed on top of the PMMA resist. The resist with the cavity structure was then lifted-off by sonicating the chip in A-Methylpyrrolidone (NMP) for 6 min, leaving aligned DNA origami arrays on the chip pre-defined by EBL (FIG. HE). The lift-off step is not necessary depending on the downstream process and application, e.g. nanomaterial binding, but can result in virtually no background contamination at the end of fabrication. The CSMOP method with the placement of a square-shaped origami structure was further validated (FIG. 1 IF).

[00126] The origami placement yield with CSMOP primarily depends on the cavity size, origami concentration, solution cation and placement time. In general, larger cavity size, higher origami concentration, and higher Mg²⁺ concentration and longer placement time lead to overall higher origami binding yield, which is consistent with the DOP method in the literature. [22, 81- 82], However, larger cavity size also leads to multiple origamis placed in the same cavity and broader origami orientation distributions. Rhombic PMMA cavity arrays of 97 x 135 nm, 106 * 150 nm and 114 x 161 nm by increasing electron beam (e-beam) doses from 670 pC/cm² (Dose 1) to 868 pC/cm² (Dose 2) and 1132 pC/cm² (Dose 3) respectively (FIG. 13a) in EBL were fabricated. Note that the cavity dimensions were measured by atomic force microscopy (AFM), which were convoluted with AFM probe size and imaging parameters. Moreover, the dimensions of the cavity opening at the top do not necessarily represent the dimensions of the cavity bottom, as the O2 plasma etching step (FIG. 11A, step v) expands the cavity opening (FIGS. 14A-14B). Nonetheless, the cavity size increase was consistent with e-beam doses used in EBL. As shown in FIG. 13B, the yield of correctly placed DNA origami monomers decreased from 85% to 61% and 11% (all N = 288) as the cavity size increased, while the percentage of two or more origami placed in one cavity increased from 3% to 27% and 86% respectively (FIG. 13C). Note that all cavity sites were occupied by DNA structures under this condition, including deformed origami and origami fragments (categorized as “Others” in FIG. 13C). More importantly, the orientation of origami monomers after resist lift-off was less controlled as the size of the cavity increased. Here, origami orientation was defined as the orientation of its long diagonal axis within range of -90° to 90°, amid the two-fold rotational symmetry of the rhombic shape. With the 97 x 135 nm cavity, 81% origami monomers were oriented horizontally as the cavities within 0 ± 5° with a standard deviation of 4° (N = 245) (FIG. 13D, graph i); while with the 106 x 150 nm cavity, only 45% origami monomers were oriented within the same range with a standard deviation of 9° (N= 175) (FIG. 13D, graph ii). To demonstrate the capacity to simultaneously determine the orientation of individual origami, an array with the optimal cavity size featuring two sets of rhombic cavities positioned at either 45° or -45° was fabricated (FIG. 13E, top left). Subsequent origami placement resulted in the same array design (FIG. 13E, top right), where 85% of origamis oriented within either 45° ± 5° or -45° ± 5° (JV = 236) (FIG. 13E, bottom) with a placement yield of 82% (N = 288). Hence, the CSMOP method is capable of positioning low-symmetry origami structures at pre-defined specific locations with orientation control on a silicon chip.

[00127] Sodium ions (Na¹ ) can reduce kinetically trapped states in CSMOP. Na¹ has been demonstrated to weaken Mg² -mediated origami binding to a negatively charged surface. [38, 93- 95], Without being bound to any particular theory, when multiple (most commonly two) origamis landed into the same cavity and both bound to the bottom surface with one edge, they could be kinetically trapped. Adding Na⁺ to the origami solution for placement can reduce origami-substrate binding affinity and promote dynamic corrections of misplacement. When using an origami solution containing 100 mM Na⁺ for CSMOP while keeping the rest of the conditions the same as above, a drastically decreased number of multiple origamis placed in the same cavity was observed (FIG. 13F). However, this also resulted in un-occupied cavity sites, whose percentage decreased as the cavity size increased. This decrease in cavity occupation rate can be mitigated by increasing origami concentration and incubation time during placement. The origami orientation control of CSMOP arrays fabricated with Na⁺ was consistent with the results above (FIGS. 15A-15B).

[00128] To demonstrate that functional materials can be templated using CSMOP, DNA functionalized gold nanorods (AuNRs) were first hybridized to the rhombic origami arrays (FIG. 16A). The CSMOP array was fabricated with rhombic origami presenting 5 ssDNA overhangs (on left in figure) arranged along the long axis. Upon DNA origami placement, a solution of AuNRs (75 nm x 18 nm) functionalized with complementary DNA strands was dropped onto the chip with the CSMOP arrays and incubated for 2 hrs at room temperature, followed by buffer washing and PMMA resist lift-off to remove excess AuNRs. AFM imaging showed that the AuNRs were assembled to the rhombic origami along its long axis (FIG. 16B). The AuNR orientation deviation from the designed alignment can be attributed to the effect of capillary forces during the drying process before PMMA lift-off. Light scattering off a AuNR depends on the incident light wavelength and the relative angle between the polarization of the incident light and the AuNR orientation. Leveraging the orientation control capability of the CSMOP method, the light scattering of individual AuNRs was able to be controlled at specific locations on the silicon chip. A 4.5 pm x 5 pm CSMOP array (FIG. 16C) consisting of four 1 pm x 5 pm strips (FIG. 16C, i- iv) was fabricated, each containing 8000 (250 nm inter-origami distance, i and iv) or 2000 (500 nm inter-origami distance, ii and iii) rhombic origami positions oriented vertically (i and ii) or horizontally (iii and iv). With one solution incubation process, AuNRs were assembled onto these origami templates placed at specific locations with orientations that could be tailored individually (FIG. 16D). Under unpolarized incident light, vertically aligned AuNRs (i and ii) primarily scattered red light along the vertical direction (i.e. analyzer direction) due to the longitudinal plasmon resonance; while horizontally aligned AuNRs primarily scattered green light from the transverse plasmon resonance mode along the analyzer direction (FIG. 16C). Individual AuNRs could be resolved in strip ii and iii where AuNRs were arranged 500 nm apart, above the optical diffraction limit. Under vertically polarized incident light (no analyzer), AuNR arrays appeared either red or green similar to the previous case, as either longitudinal or transverse plasmon resonance mode dominated the light scattering depending on the relative angle between the incident light polarization direction and the AuNR orientation (FIG. 16E, top left). After switching the incident light polarization direction to 45°, both vertically and horizontally aligned AuNRs showed the same yellow color under dark -field microscope (FIG. 16E, top right), which is a mixture of roughly equal amount of red light and green light. When using an incident light of horizontal polarization direction (FIG. 16E, bottom), the scattered light color switched where vertically aligned AuNRs scattered green light and horizontally aligned AuNRs scattered red light. The programmable angle dependent optical property of AuNRs templated by CSMOP can be used for microscale anti-counterfeiting labeling [96-97] or data storage. [98-102],

[00129] The dehydration-assisted method for functionalizing QDs and QRs with DNA can be used to integrate them seamlessly into CSMOP arrays, advancing the development of nextgeneration photonic devices. More importantly, a shape-matching CSMOP strategy has been developed to incorporate different device components in one fabrication process (FIGS. 17A-17C). Diverse DNA origami shapes, guiding different functional materials, can be precisely arranged on a circuit substrate in an orthogonal manner. The shape-matching feature ensures that origami of a specific shape perfectly aligns with its corresponding cavity or landing pad, maximizing binding energy. This approach not only facilitates the integration of nanomaterials that are currently inaccessible with conventional lithography methods for controlled arrangement at nanoscale (such as colloidal QDs and QRs,), but also significantly reduces the time and resources required for fabricating complex multicomponent devices by orders of magnitude.

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[00131] Details of one or more embodiments are set forth in the accompanying drawings and description. Other features, objects, and advantages will be apparent from the description, drawings, and claims. Although a number of embodiments of the invention have been described, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. It should also be understood that the appended drawings are not necessarily to scale, presenting a somewhat simplified representation of various features and basic principles of the invention.

Claims

WHAT IS CLAIMED IS

1. A method of forming a DNA functionalized complex comprising: mixing thiolated DNA with a plurality of an inorganic moiety in an organic solvent to form a mixture; and dehydrating the mixture to form the DNA functionalized complex.

2. The method of claim 1, further comprising recovering the DNA functionalized complex.

3. The method of claim 1, wherein dehydrating the mixture includes adding an alcohol to the mixture.

4. The method of claim 1, wherein the alcohol includes a C1-C8 alcohol.

5. The method of claim 3, wherein C1-C8 alcohol is 1-butanol.

6. The method of any one of claims 1-4, wherein the inorganic moiety includes a metal complex, a nanosphere, a nanorod, or other nanoshape.

7. The method of any one of claims 1-5, wherein the inorganic moiety includes a nanoparticle having a size of less than 50 nm, less than 40 nm, less than 30 nm, less than 20 nm, or less than 10 nm.

8. A method of forming a 2D nanoparticle array comprising: tiling a plurality of DNA functionalized inorganic moi eties on a surface in a regular controlled pattern.

9. The method of claim 8, wherein tiling includes assembling DNA functionalized inorganic moi eties in a controlled orientation on the surface.

10. The method of claim 9, wherein the array includes a wireframe DNA origami structure or assembly of multiple DNA origami structures.

11. The method of claim 10, wherein the wireframe DNA origami structure includes a crossover design or hybridization or base-stacking or other interfacial self-assembly design.

12. The method of claim 8, wherein the inorganic moieties are assembled to origami lattices with controlled positions, inter-particle distances and orientations.

13. The method of claim 12, wherein the origami lattices with controlled positions can have a programmable and specified loading yield over 10%, over 20%, over 30%, over 40%, 50%, over 60%, over 70%, over 80%, or over 90%.

14. The method of claim 8, wherein the array includes a monolayer nanoparticle face-selecting overhangs.

15. The method of claim 8, wherein the array includes rhombic, square, scalene triangle, isosceles triangle, equilateral triangle, rectangular, trapezoid, pentagonal, hexagonal, heptagonal, or octagonal DNA origami.

16. The method of claim 15, wherein the DNA origami self-assembles into a 2D lattice face up.

17. The method of claim 8, wherein the controlled pattern self-assembles either randomly or due to electrostatic interactions or DNA hybridization interactions between the surface and an origami or other affinity reagent, or by steric or other non-specific interactions that induce faceup self-assembly.

18. The method of any one of claims 8-17, further comprising annealing the array.

19. The method of claim 18, wherein annealing the array includes thermally annealing either with or without mechanical or other vibration or shaking to enhance self-assembly kinetics and/or yield.

20. The method of any one of claims 1-19, wherein the nanoparticles include gold, InP, CdSe, CdTe, CdS, ZnS, ZnSe, Ag2Te, Ag2Se, A 2S, PbS, PbSe, CdSe/CdS core/shell, CdSe/ZnS core/shell, ZnSe/ZnS core/shell, alloyed CdSeS, alloyed CdSeTe, or alloyed CdZnSe.

21. An array comprising a plurality of inorganic moi eties aligned in a monolayer 2D array with a controlled spacing and orientation between each inorganic moieties arising from a DNA origami lattice on a substrate.

22. A method for fabricating aligned colloidal semiconductor nanocrystal arrays on a two dimensional (2D) solid surface comprising surface-assisted large scale assembly of components.

23. The method of claim 22 wherein said aligned colloidal semiconductor nanocrystal arrays are periodic in 2D space, and if the colloidal semiconductor nanocrystal is anisotropic in shape (i.e. non-spherical), its orientation is aligned with its periodic replicates across the 2D space.

24. The method of claim 22 wherein said aligned colloidal semiconductor nanocrystal arrays are

1) infinite across a 2D surface; or

2) finite as size and shape defined regions on a surface.

25. The method of claim 22 wherein said colloidal semiconductor nanocrystals are aligned using nucleic acid structures as a template, wherein the colloidal semiconductor nanocrystal attaches to a nucleic acid structure monomer at a specific location, and if the colloidal semiconductor nanocrystal is anisotropic in shape (i.e. non-spherical), it binds to the nucleic acid structure with a pre-defined orientation.

26. The method of claim 22 wherein said nucleic acid structure template is aligned in an array by

1) assembling into a 2D lattice superstructure on a surface; and/or

2) attaching to location and orientation prescribed shape-matching landing pads on a surface.

27. The method of claim 22 wherein said nucleic acid structure array contains one or more unique nucleic acid structure geometries, wherein each nucleic acid structure geometry templates one or more types of colloidal semiconductor nanocrystals with one or more pre-defined orientations.

28. The method of claim 22 wherein said colloidal semiconductor nanocrystal is a quantum dot (QD) or a quantum rod (QR).

29. The method of claim 22 wherein said nucleic acid structure is a wireframe DNA origami.

30. The method of claim 22 for fabricating QD and QR 2D arrays with a nucleic acid structure 2D lattice comprising the steps of:

1) functionalizing QDs and QRs with a dense layer of DNA sequence, wherein the QDs and QRs are functionalized and phase-transferred in a single step and remain stable;

2) fabricating 2D DNA origami lattice templates on surface, wherein the origami units in the lattice present uniformly addressable binding sites for DNA hybridization; and

3) assembling DNA-functionalized QDs and QRs to said origami lattice template via DNA hybridization, wherein the QDs and QRs are aligned in space and orientation.

31. The method of claim 30 wherein step 1) is accomplished by an ultrafast dehydration-assisted DNA conjugation method comprising the steps of:

1) Mixing QDs/QRs dispersed in organic solvent with thiol -derivatized DNA in aqueous solution and sodium salt solution;

2) Ultrasonicating the mixture until emulsion is observed;

3) Adding 1 -butanol to dehydrate the mixture; and

4) Adding aqueous buffer to rehydrate and recover the DNA functionalized QDs/QRs.

32. The method of claim 31 wherein the QDs/QRs dispersed in organic solvent in step 1) are any semiconductor nanocrystals of group II- VI {e.g. CdS, CdSe, CdTe, ZnS, ZnSe, ZnTe), group IV-V1 {e.g. PbS, PbSe), group I-VI {e.g. Ag2S, Ag2Se, Ag2Te) or group 1-III-VI {e.g. AglnS, AglnSe, CuInS, CuInSe), or their core-shell structured composites, capped with trioctylphosphine oxide (TOPO), octadecylamine, or oleic acid ligand, dispersed in common organic solvents {e.g. hexane, toluene, chloroform).

33. The method of claim 31 wherein the thiol-derivatized DNA in step 1) are single stranded or double stranded oligo nucleic acids of any sequence with one or greater number of thiol functional groups conjugated to either the 5’ or the 3’ terminal of the nucleic acid molecule.

34. The method of claim 31 wherein the final sodium salt concentration in step 1) is lOOmM regarding to the sodium ion.

35. The method of claim 31 wherein the molar ratio of thiol-derivatized DNA to QDs/QRs in step 1) is greater than 0.8 (/nm²) x the surface area (nm²) of the QD/QR used.

36. The method of claim 31 wherein the ultrasonication in step 2) takes about 5 min in an ultrasonicator.

37. The method of claim 31 wherein the volume of 1-butanol added in step 3) is more than 12 times the final volume of the mixture in step 1).

38. The method of claim 31 wherein the aqueous buffer added in step 4) is any commercially available alkaline buffer with a pH of 7-9.

39. The method of claim 31 wherein the volume of the aqueous buffer added in step 4) is 1/3 the volume of the 1-butanol added step 3).

40. The method of claim 31 wherein QDs/QRs are functionalized with DNA strands and phase- transferred from organic solvents to aqueous solutions at a record fast speed with a total processing time less than 20 min.

41. A composite synthesized via the method of claim 31 comprising a QD/QR and a corona of closely packed DNA strands conjugated to its surface with a record high DNA loading density.

42. The composite of claim 41 wherein the composite is stable in aqueous solution with a high salt concentration (e.g. IM sodium ion or 12.5mM magnesium ion).

43. The composite of claim 41 wherein it can hybridize to DNA origami structures with higher efficiency than DNA functionalize QDs/QRs produced with other methods.

44. The method of claim 31 wherein step 2) is accomplished by a Surface-Assisted Large-Scale Assembly (SALSA) method comprising the steps of:

1) folding DNA origami tiles, wherein the tiles possess lateral in-plane affinity to each other; 2) mixing said tiles with NaCl solution;

3) incubating said mixture in contact with a solid surface while annealing thermally; and

4) washing the solid surface to remove unbound substances.

45. A DNA origami structure for the method of claim 44 comprising: 1) a wireframe planar shape with parallel edges where the edges are a 6-helix bundle structure of DNA;

2) short crossover DNA overhangs with unique sequences extended in-plane from half of the edges wherein these edges are not parallel to each other;

3) hybridization vacancies on the rest of the edges at the same corresponding locations wherein said crossover DNA overhangs on their parallel counterparts can hybridize to the vacancies, creating anti-parallel crossovers between tiles;

4) short binding DNA overhangs extended out-of-plane to one side of the tile, wherein the overhang sequence is complementary to that of the DNA strands on the composite of claim 40; and 5) short face-selecting single stranded DNA overhangs extended out-of-plane to the same side of the tile as said binding DNA overhangs.

46. The method of claim 44 wherein the final concentration of the origami tile is 500pM and the final concentration of NaCl is 0.5M in step 2).

47. The method of claim 44 wherein the solid surface in step 3) is a freshly cleaved mica surface.

48. The method of claim 44 wherein the thermal annealing in step 3) is performed on a hotplate shaker with 12 cycles of consecutive heating at 60°C, 55°C, 50°C for 1 hr each (36 hr in total) with 200 rpm shaking, and then letting the setup cool down to room temperature undisturbed.

49. The method of claim 44 wherein the washing is accomplished by rinsing the mica surface with 100pL buffer dropwise for 16 times.

50. The method of claim 30 wherein step 3) is accomplished by incubating the composite of claim 41 with a washed mica surface for over 4 hrs.

51. The method of claim 30 wherein step 3) further comprises: washing the incubated mica surface with lOOpL buffer dropwise for 16 times, incubating the surface with lOmM NiCh solution for 10 min, washing the surface 3 times with lOOpL, and drying with a flow of compressed air.

52. A superstructure of aligned semiconductor arrays comprising:

1) a solid substrate surface;

2) a two-dimensional nucleic acid structure lattice; and

3) colloidal semiconductor nanocrystals bound to nucleic acid structures.

53. The superstructure of claim 52 wherein the two-dimensional nucleic acid structure lattice is assembled directly on the solid substrate surface with the nucleic acid structure monomers.

54. The superstructure of claim 52 wherein the nucleic acid structure monomers within said lattice presents periodic and uniformly aligned binding nucleic acid overhangs extended away from said solid surface.

55. The superstructure of claim 52 wherein the colloidal semiconductor nanocrystals bind to said nucleic acid structure lattice through nucleic acid hybridization and align

1) locally by the shape-matching arrangement of the overhangs on said nucleic acid structure monomers, if the semiconductor is anisotropic; and

2) periodically by the repeating binding nucleic acid overhangs in each monomer in said lattice.

56. The method of claim 22 for fabricating QD and QR 2D arrays with prescribed landing pads on surface comprising the steps of:

1) prescribing location and orientation prescribed shape-matching landing pads on surface;

2) attaching said DNA origami structure of claim 44 to said landing pads; and

3) assembling said composite of claim 40 to said DNA origami structure attached to said landing pads.

57. The method of claim 56 wherein step 1) is accomplished by prescribing DNA-binding landing pads via lithography methods, wherein the landing pads are of various sizes and shapes.

58. The method of claim 56 wherein step 2) is accomplished by attaching one or more DNA origami structures of matching sizes and shapes to said landing pads, wherein an annealing process is employed to attach more than one class of origamis with different shapes to their corresponding landing pads in the same process orthogonally, via shape-matching.

59. The method of claim 56 wherein step 3) is accomplished by assembling one or more types of DNA-functionalized QDs/QRs to said DNA origami structures on said landing pads presenting complementary DNA sequences.

60. A method of fabricating controlled arrays on a two dimensional (2D) solid surface comprising: preparing a substrate to include a pattern of shapes; and depositing a plurality of DNA origami structures in the pattern of shapes.

61. The method of claim 60, wherein the pattern of shapes is formed with a mask material.

62. The method of claim 61, further comprising forming the shapes in the mask material.

63. The method of claim 62, further comprising etching an exposed area of the shape on the substrate.

64. The method of claim 63, further comprising removing the mask material after depositing the DNA origami structures.

65. The method of claim 60, further comprising exposing the deposited DNA origami structures in the pattern of shapes to a nanocrystal material having an affinity for the DNA origami structures.

66. The method of claim 60, wherein the DNA origami structures include a nanocrystal material.

67. The method of claim 60, further comprising depositing the plurality of DNA origami structures in the pattern of shapes includes exposing the structures to a solution including a monovalent cation.

68. The method of claim 60, wherein the plurality of DNA origami structures have one or more geometries that match with one or more shapes of the pattern of shapes.