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Epitaxy: Programmable Atom Equivalents Versus Atoms

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† § ⊥ ‡ †Department of Chemical and Biological Engineering, ‡International Institute for Nanotechnology, §Department of Chemistry, and ⊥Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
∥ Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
⊗ Thomas J. Watson Laboratories of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
# X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
*E-mail: [email protected]
*E-mail: [email protected]
Cite this: ACS Nano 2017, 11, 1, 180–185
Publication Date (Web):December 5, 2016
https://doi.org/10.1021/acsnano.6b06584

Copyright © 2016 American Chemical Society. This publication is licensed under these Terms of Use.

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Abstract

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The programmability of DNA makes it an attractive structure-directing ligand for the assembly of nanoparticle (NP) superlattices in a manner that mimics many aspects of atomic crystallization. However, the synthesis of multilayer single crystals of defined size remains a challenge. Though previous studies considered lattice mismatch as the major limiting factor for multilayer assembly, thin film growth depends on many interlinked variables. Here, a more comprehensive approach is taken to study fundamental elements, such as the growth temperature and the thermodynamics of interfacial energetics, to achieve epitaxial growth of NP thin films. Both surface morphology and internal thin film structure are examined to provide an understanding of particle attachment and reorganization during growth. Under equilibrium conditions, single crystalline, multilayer thin films can be synthesized over 500 × 500 μm2 areas on lithographically patterned templates, whereas deposition under kinetic conditions leads to the rapid growth of glassy films. Importantly, these superlattices follow the same patterns of crystal growth demonstrated in atomic thin film deposition, allowing these processes to be understood in the context of well-studied atomic epitaxy and enabling a nanoscale model to study fundamental crystallization processes. Through understanding the role of epitaxy as a driving force for NP assembly, we are able to realize 3D architectures of arbitrary domain geometry and size.

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The epitaxial deposition of thin films has been key to the semiconductor industry in its efforts to control material properties as a function of crystal structure. The transfer of order and orientation from a substrate to a deposited crystal is dependent upon many interlinked variables (e.g., interfacial chemical potential, crystal lattice parameters, defect stability) that vary as a function of both atomic composition and deposition protocol. (1-3) As a result, significant effort has been expended to fully understand atomic epitaxy, leading to a wealth of information about thin film crystallization behavior. For nanoscale systems, many strategies have also been developed to assemble nanomaterials into thin films; (4-8) however, these methods often lack the ability to precisely control the overall 3D structure of the resulting crystals (e.g., size, shape, and orientation).
Recent developments in nanoparticle (NP) assembly have shown that NPs functionalized with a dense monolayer of oligonucleotides can form ordered superlattice structures with programmable lattice parameters and crystallographic symmetries, and these building blocks exhibit many crystallization behaviors similar to those observed in atomic systems. (9-11) Thus, these “programmable atom equivalents” (PAEs) hold promise for tailoring material structure at the nanoscale in a precise and controllable manner. In the context of PAE thin films, assembly on unpatterned surfaces has been demonstrated to produce rough, polycrystalline films with a lack of long-range order or alignment. (12) Assembly of PAEs on patterned substrates has also been attempted but was limited to monolayers of single crystalline thin films, as the combination of both NP–substrate and NP–NP binding events significantly increases the complexity of multilayer epitaxial crystal formation. (4, 13, 14) In order to fully control thin film morphology in PAE superlattices, these complexities must be better understood via investigations into the thermodynamics of lattice growth as a function of different variables. The fundamental information gained from these comprehensive studies not only provides the opportunity to develop superlattice morphologies with complex 3D structures but also has the potential to provide insight into the process of atomic thin film epitaxy.
Like atomic systems, there are many design parameters that can affect multilayer epitaxy, such as factors inherent to the deposition protocol (e.g., thermal annealing temperature) and factors dictated by PAE design (e.g., DNA hybridization strength). (10, 12, 15) However, unlike atomic epitaxy where only the deposition protocol can be modulated, parameters related to the individual PAE building blocks can be precisely controlled as a function of DNA, (9, 10, 12) particle, (16-19) or substrate pattern design. (13) Fully understanding how PAE epitaxy can be manipulated as a function of these variables will potentially yield single-crystal superlattices with controlled 3D geometries, allowing for the realization of materials possessing the desired optical, (20-22) electronic, (23) and magnetic responses. (24) Here, we report a stepwise method for synthesizing large epitaxial thin films of PAEs up to 10 layers thick and 500 μm wide and show that the corresponding growth process mimics atomic thin film epitaxy, allowing us to study epitaxy as a driving force for building a nanomaterial as it evolves from a 2D monolayer to a 3D crystal lattice.

Results and Discussion

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Epitaxial growth of NP superlattices was realized by depositing PAEs layer-by-layer onto lithographically defined substrates designed to resemble a continuous (100) plane of a body-centered cubic (bcc) lattice (Scheme 1). Using standard electron-beam lithography (EBL) techniques, 500 μm × 500 μm arrays of gold posts were synthesized on a silicon wafer, such that post diameters and post-to-post distances were comparable to the PAE NP core diameters and the lattice parameter of the superlattice. These posts were functionalized with DNA and hybridized with complementary DNA linkers that presented a single-stranded recognition region to which PAEs could bind. Stepwise thin film growth was done via successive immersion of the template into suspensions of PAEs displaying a single-stranded recognition region complementary to that of the previous layer. They were then embedded in silica and characterized by synchrotron-based small-angle X-ray scattering (SAXS, Figure 1 middle) and grazing incidence small-angle X-ray scattering (GISAXS) to determine the overall degree of epitaxy. (25) Lattices were also examined by scanning electron microscopy (SEM, Figure 1 top), which allowed for real-space imaging of superlattice surface morphology; focused ion beam milling was used to etch selected sections of the silica-embedded lattices, allowing for SEM characterization of the internal structure (FIB-SEM, Figure 1 bottom).

Scheme 1

Scheme 1. Layer-by-Layer Assembly of PAE Superlattice Thin Films on a DNA-Functionalized Template
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Figure 1

Figure 1. SEM, SAXS, and FIB-SEM characterization of DNA–NP thin films. (a) 2-, 5-, and 10-layer DNA–NP thin films assembled at 25 °C exhibit kinetic roughening and nonepitaxial growth beyond four layers of deposited PAEs. (b) 5- and 10-layer DNA–NP thin films assembled at 25 °C and thermally annealed after the full deposition process demonstrate enhanced ordering, but only the 5-layer sample is fully epitaxial since only PAEs that are close to the initial four epitaxial layers experience sufficient driving force to align with the patterned template. (c) 10-layer DNA–NP thin film where each layer is assembled at an elevated temperature; this process produces smooth, crystalline thin films fully epitaxial with the patterned substrate. Scale bars for SEM and FIB-SEM are 500 and 200 nm, respectively.

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We first investigated the deposition of particles onto templated substrates via far-from-equilibrium conditions (i.e., low growth temperature) to understand the effectiveness of the EBL-patterned template itself as a driving force for multilayer epitaxy. When compared to atomic systems, this low temperature deposition is analogous to chemical bath deposition, where atoms rapidly precipitate from solution, resulting in disordered materials. (26) Here, when conducting templated PAE deposition at 25 °C, initial layers conform epitaxially to the substrate, but subsequent layers transition to a kinetically roughened, glasslike state (Figure 1a). This can be observed in the SAXS data, where a sample with two deposited layers shows diffraction spots (corresponding to aligned, single-crystal bcc lattices), while 5- and 10-layer films exhibit diffuse scattering, corresponding to disordered PAE aggregates. The relative degree of epitaxy (XA) at each layer was determined by comparing the SAXS intensity of the spots from the (110) peak of the epitaxial PAEs and the intensity of the diffuse ring (Figure S1), where an XA value of 1 indicates complete epitaxy of the PAEs; the value of XA decays from 0.99 to 0.88 after 5 layers and to 0.65 at 10 layers (Figure 2a). This was corroborated by the FIB-SEM cross-sectional images, which showed that the first few layers of all samples are indeed epitaxial, up to a critical layer number of ∼4, with PAEs above the critical layer adopting a kinetic, glassy state (Figure 1a, bottom, and Figure S2). This is a morphological transition commonly observed in atomic thin films, which exhibit temperature-dependent surface roughening when the adsorption rate is faster than the reorganization rate. (2) Similarly, PAEs adsorbed at low temperature are stuck in kinetic traps, leading to an accumulation of defects in the film, which increases the surface area available for subsequent NPs to bind. This results in amorphous, rough films; the root-mean-squared roughness (RRMS) increases by 140% from 2- to 10-layer deposited films (Table S2). The rapid, nonlinear increase in height, as measured by the mean z-distance of topmost NPs from the substrate, is further indication of nonequilibrium growth (Figure 2b). These data clearly show that the EBL template does serve as a strong driving force for epitaxy, but this driving force rapidly decays with increasing layer number when lattices are assembled at nonequilibrium conditions.

Figure 2

Figure 2. Quantitative characterization of films shows that depositing PAEs at near-equilibrium conditions induces (a) higher degree of epitaxy (as determined by SAXS) and (b) more controlled growth and a smoother film morphology (as determined from FIB-SEM).

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It is possible to reorganize thin films into more thermodynamically preferred configurations by adding thermal energy. This is done frequently in atomic systems to turn disordered or polycrystalline thin films (e.g., from sputter coating) into a film with a single-crystal orientation. This annealing process was mirrored in the PAE system by first depositing 5 and 10 layers at 25 °C and then heating the sample slightly below the film’s melting temperature (Tm, the temperature at which the superlattice dissociates). Interestingly, in the process of determining the films’ Tm, it was observed that they exhibit thickness-dependent melting point depression, analogous to atomic thin film systems (Figure S3). The thermal stability of the film, measured by monitoring lattice decomposition using SAXS, showed a concomitant increase with thickness due to the decreasing surface-to-volume ratio, as described by Lindemann’s criterion and the Gibbs–Thomson relationship. Upon annealing the samples at (Tm – 2) °C, the 5-layer film became crystalline and epitaxial while retaining the same height and RRMS. On the other hand, the 10-layer sample became crystalline, but not epitaxial (Table S2 and Figure 1b). This is most likely due to the fact that the previously observed critical layer thickness for epitaxy is ∼4, indicating that, in the 5-layer sample, only the topmost layers of NPs were disordered. The differences in epitaxy for these two samples mirror previous findings for nonepitaxial PAE systems, in which post-assembly annealing is capable of inducing crystallization but grain boundaries are difficult to remove once formed. (15)
The greatest degree of ordering in thin films can be achieved when the entire deposition process occurs under near-equilibrium conditions. To achieve this in atomic systems, molecular beam epitaxy is performed at high temperatures where deposition and desorption occur at equivalent rates, allowing each adatom to find its thermodynamic position in the monolayer before the next layer is introduced. To achieve this effect in the PAE system, each layer was deposited at an optimized growth temperature (Tm – 4) °C. With this method, nearly perfect Frank–van der Merwe (layer-by-layer) growth was observed, with films remaining epitaxial (XA = 0.99) far beyond the critical layer thickness of room-temperature growth (Figures 1c and 2a). Film cross-sections examined with FIB-SEM show smooth surfaces with an absence of kinetic roughening; the RRMS of the 10-layer film is 51% less than that of the equivalent film assembled at 25 °C (Table S2). Film height increases linearly with deposition layer, indicating that deposition occurred under equilibrium conditions (Figure 2b). Both GISAXS and SAXS confirmed that the film is well-ordered over a large area and nearly completely epitaxial with the patterned template (Figure 1c, middle, and Figure S4). Notably, a loss of radial broadening in the SAXS pattern, corroborated by FIB-SEM, indicates that as the film grows from 2 to 5 layers the stability of the PAE network increases to such a point that the particles become locked within a single domain. The appearance of thin lines of diffuse scattering between the peaks originates from the vibrational motion of the particles (Figures S5 and S6). This equilibrium growth condition was therefore able to create a crystalline film of well-defined and arbitrary crystal habit that is epitaxial over a domain of 500 μm (Figure 3 and Figure S7).

Figure 3

Figure 3. Optical image of DNA-functionalized NP thin film grown from a template exhibiting an arbitrary geometry. SEM images show that the thin film possesses the same crystallographic orientation across the entire structure.

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Finally, an interesting aspect of this PAE system that does not have an atomic analogue is the ability to tune interfacial potential. In atomic crystals, chemical potentials between adatoms and the substrate are influenced by atomic identity and crystallographic symmetry. However, in PAEs, the chemical potential between NPs and the substrate can be tuned by adjusting DNA bond strength; we have recently demonstrated that this can be accomplished after assembly using DNA intercalators. (27, 28) Here, these intercalators can be used to “staple” each PAE layer after deposition and annealing, thereby increasing their binding strength and preventing reorganization during subsequent cycles of growth. When this stapling method was employed, 10-layer thin films exhibited similarly high epitaxy (XA = 0.99) but 66% higher RRMS than the nonintercalated counterpart, which can be attributed to defect immobilization by the intercalators (Figures S2 and S8 and Table S2). These data and the observed thickness-dependent melting point depression indicate that thermal annealing after each round of deposition induces reorganization not only in the topmost layer of PAEs but also in subsurface layers. This reorganization is critical for achieving perfect epitaxy, indicating the importance of being able to precisely modulate PAE binding strength during deposition.

Conclusion

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In this work, we have determined that DNA-mediated NP crystallization follows similar thin film growth processes that are observed in atomic thin films, but importantly, PAEs offer a set of parameters distinct from atomic systems that can be independently tuned to control crystallization outcome. Unlike atomic systems, epitaxy can be controlled lithographically and through the choice of oligonucleotide bonding elements. These observations allow one to grow precisely defined crystalline NP architectures of arbitrary shape and size over thousands of μm2. Future studies will be able to take advantage of the tunable nature of the bonding interactions between the PAEs and the substrate to investigate how different parameters (DNA sequence, grafting density of DNA on PAEs) affect the epitaxial deposition process, laying the groundwork for making functional device architectures from crystalline NP networks.

Methods

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DNA Functionalization of Gold Nanoparticles

DNA functionalization on gold nanoparticles (AuNPs, 20 nm diameter from Ted Pella) was done using previously described methods. (10, 27) The 3′ propylmercaptan protecting group of the thiolated DNA (Table S1) was cleaved with 100 mM dithiolthreitol (Sigma-Aldrich) for 1 h, followed by desalting on a NAP5 size-exclusion column (GE Healthcare). The deprotected DNA was combined with colloidal AuNPs in a ratio of 6 nmol of DNA per 1 mL of gold colloid. After a 30 min incubation, 1 wt % sodium dodecyl sulfate was added to bring the solution concentration to 0.01%. NaCl (5 M) was added stepwise, followed by 10 s of sonication after each salt addition, until the final concentration of 0.5 M NaCl was achieved. The solution was then allowed to incubate in a shaker overnight to maximize the DNA loading (140 rpm, 37 °C). Unbound DNA and excess salt were removed by four successive rounds of centrifugation and resuspension in nanopure water using a 100 kDa filter centrifuge tube (Millipore) on a swinging bucket centrifuge (2500 rpm, 5 min). After the last round of centrifugation, the DNA–NPs were concentrated down to the total volume of 500 μL. The concentrations of resulting DNA-NPs were determined using a Cary 5000 UV–vis–NIR spectrophotometer (Agilent) and known extinction coefficients from Ted Pella.

Substrate Preparation and Functionalization

Patterned Template Synthesis

Si wafers with native oxide (⟨100⟩, B doped, 10 Ω·cm (Silicon Quest International)) were cleaned (2 min acetone rinse, 2 min methanol rinse, drying under nitrogen) and baked for 2 min at 180 °C. PMMA resist (495-A4) was spun onto the wafers (3500 rpm for 60 s) and postbaked (5 min at 180 °C). Once they were cooled, 950-A2 PMMA resist was spun coat onto the coated wafers at 3500 rpm for 1 min to create a bilayer and postbaked (5 min at 180 °C). EBL was used to write the desired pattern with an optimized beam current (500–700 pA) and dose range (640–1500 μC/cm2). The substrates were developed in cold MIBK/IPA in a 1:3 ratio for 60 s, briefly rinsed in IPA, and dried under nitrogen. The posts were then deposited using an electron-beam evaporator: 3 nm of Cr at a rate of 0.5 Å/s followed by 30 nm of Au at a rate of 1 Å/s. Wafers were then diced into pieces with one pattern per chip. Liftoff was done in heated (100–150 °C) PG remover (Microchem); the chips were then rinsed (acetone followed by IPA) and finally dried under nitrogen.

Silanization of Patterned Templates

A hydrophobic hexamethyldisilazane (HMDS, Sigma-Aldrich) coating was employed to prevent nonspecific adsorption of DNA–NPs to the silicon chip, so that DNA–NP assembly occurred only on the DNA-functionalized Au posts of the template. This is a widely used vapor coating technique where the Si of HMDS reacts to form a strong bond with the oxidized silicon, creating a hydrophobic surface. Substrates were prebaked in a Vulcan 3-550 burnout furnace for 1 h at 150–200 °C to remove adsorbed water molecules. Silanization was performed by incubating the prebaked substrates in a sealed, dry chamber with a small open beaker containing 5 mL of HMDS and 5 mL of anhydrous hexane (Sigma-Aldrich) for 24 h. After 24 h, the substrates were rinsed and sonicated in water or ethanol for a few seconds.

Unpatterned Substrate Preparation

Unpatterned substrates were prepared by depositing a 2 nm Cr adhesion layer followed by 8 nm of Au on Si wafers using a PVD 75 E-beam evaporator (Kurt J. Lesker) at a base pressure of 5 × 10–8 Torr. Cr and Au were evaporated at the rates of 0.3 and 0.5 Å/s, respectively. These conditions yielded a smooth Au film, which is crucial for the crystalline DNA–NP thin film growth.

Substrate DNA Functionalization

DNA functionalization of substrates was performed by incubating each substrate in 2 mL Eppendorf tubes (Fisher Scientific) containing 5 μM HS-A DNA solution diluted in buffer A (0.5 M NaCl, 10 mM phosphate buffered saline (PBS)) overnight. The propylmercaptan protecting group on the thiolated DNA was cleaved prior to the functionalization, as described above. The substrates were then washed three times in buffer A with vigorous agitation to remove unbound DNA and then hybridized with “linker” sequences (Table S1). “Linkers” consist of one complementary section that hybridizes to the thiolated DNA sequence, two double-stranded “duplexed” regions, and a short single-stranded sticky end. To prepare the duplexed linker stocks (100 μM), “duplexer” strands were added to linkers A and B in a 2:1 molar ratio in 0.5 M NaCl. The linkers were heated up to 70 °C for 5 min and cooled to room temperature over 4 h to achieve full hybridization. Duplexed linker stock solutions of 100 μM concentration were made fresh every few weeks. Complementary linker (linker A) was hybridized to the DNA-functionalized substrate by incubating substrates in 0.5 μM duplexed linker A solution at 0.5 M NaCl at 35 °C for 4 h. Prior to layer-by-layer growth of DNA–NPs, the substrates were rinsed five times in buffer A.

Layer-by-Layer DNA–Nanoparticle Superlattice Thin Film Assembly

Determining the Thin Film Annealing Temperature

To find the appropriate annealing temperature for the DNA–NP thin films, it is first necessary to determine the Tm of DNA–NP aggregates. Although the thermal melting and desorption behaviors are slightly different for solution-phase aggregates versus thin films, the Tm DNA–NP aggregates can be used as a quick way to inform thin film assembly and annealing temperature. NP superlattice aggregates were prepared by mixing 0.5 pmol of DNA-functionalized 20 nm AuNPs (HS-A and HS-B) and 400 equiv per particle of each duplexed linker in a final concentration of 0.5 M NaCl at room temperature. Assembly was mediated by the complementary pendant “sticky ends” displayed on the linkers. After the sample was allowed to aggregate over 5–10 min, the thermal melting behavior was monitored using a Cary 5000 UV–vis–NIR spectrophotometer. The extinction of the solution was monitored at 520 and 260 nm while the solution was heated from 25 to 60 °C at a ramp rate of 0.25 °C/min, and Tm was calculated from the point of inflection of the melting curve. Typically, reorganization and crystallization can be achieved by annealing a thin film superlattice at 2 °C below Tm,aggregate for 15 min. This is experimentally determined by confirming the crystallinity of annealed DNA–NP thin films grown on unpatterned substrates using SEM (Figure S9).

DNA–NP Superlattice Thin Film Assembly

A- and B-type DNA–NP assembly solutions were made by hybridizing each type of NP with its corresponding linker DNA (duplexed as described above) at 400 linkers per NP and incubated at 35 °C for 5 min. The NPs were subsequently diluted to 1 nM concentration (0.5 M NaCl, 10 mM PBS) and used for five layers of PAE assembly. DNA–NP superlattices were grown from the patterned substrates in a layer-by-layer fashion using four different growth conditions: (1) low-temperature growth, (1) low-temperature growth followed by annealing step, (3) elevated temperature growth, and (4) same conditions as 3 with an intercalation step after each annealing step. The intercalator solution was prepared by diluting [Ru(dipyrido[3,2-a:2′,3′-c]phenazine)(4,4′-dimethyl-2,2′-bipyridine)2]Cl2 in 10 mM PBS buffer. This compound was synthesized according to previously reported methods. (29) For further details on the individual growth conditions, see Table S3. Layer-by-layer assembly was accomplished in the following way. Substrates functionalized with A-type DNA were incubated in a suspension of B-type DNA–NPs for 4 h. Then the substrates were washed five times in buffer A and immersed in A-type DNA-functionalized AuNP for 4 h. This constituted two layers of DNA–NPs. For the annealing step, the substrate was incubated in buffer A at an elevated temperature for 15 min. This process was repeated until the desired number of layers was achieved. After the desired number of layers was reached, the samples were stored in buffer A at 25 °C.

Silica Embedding

In order to transfer liquid-phase thin film superlattices to the solid state for characterization by SEM and GISAXS while preserving the structure, samples were embedded in silica using a sol–gel process. (30) First, 3 μL of N-(trimethoxysilyl)propyl-N,N,N-trimethylammonium chloride (TMSPA, Gelest, 50% in methanol) was added to the thin film superlattices in 1 mL of buffer A and left to fully associate with the DNA bonds within the superlattices for 30 min on an Eppendorf Thermomixer R (1400 rpm, 25 °C). Then 5 μL of triethoxysilane (Sigma-Aldrich) was added, and the sample was shaken for another 30 min before being removed. The samples were rinsed with running water and blown dry with N2. In the case of unsuccessful silica embedding, NPs will dissociate during the rinsing step. In order to prevent such failure, it is crucial to use dry, relatively fresh silane solutions (stored in a desiccator).

Small-Angle X-ray Scattering

All SAXS and GISAXS experiments were conducted at the 12ID-B station at the Advanced Photon Source (APS) at Argonne National Laboratory. The samples were probed using 14 keV (0.8856 Å) X-rays, and the sample-to-detector distance was calibrated with a silver behenate standard. The beam was collimated using two sets of slits, and a pinhole was used. The beam size was ∼200 μm × 50 μm. Scattered radiation was detected using a Pilatus 2 M detector.

SAXS Experimental Conditions

Unembedded samples were probed using a vertical sample holder made from two coverslips that allowed a buffered environment to be maintained around the sample to preserve DNA hybridization. Embedded samples were mounted on a horizontal sample holder allowing for movement in the in-plane direction (normal to the beam). Sector averaging of diffraction patterns was used to determine the degree of epitaxy (Figure S1).

Grazing Incidence SAXS

Embedded samples were aligned to the beam on a sample positioning stage in the x (parallel to the beam), y, z (normal to the substrate), θ (rotation around the y-axis), and φ (rotation around the z-axis) directions. The sample was centered in the X-ray beam by aligning the pattern to the center of the goniometer’s θ and φ rotations and by adjusting the sample height to be normal to the φ rotation axis. Data were collected at incident angles of 0.1°. After alignment of the sample, scans were taken at several The sample was centered in the X-ray beam by aligning the pattern to the center of the goniometer's θ and φ rotations and by adjusting the sample height to be normal to the φ rotation axis. angles (rotation around the z-axis). In-depth information about GISAXS analysis is available from Senesi et al. (12) and Li et al. (25) GISAXS scattering patterns of 5-layer (Figure S4a) and 10-layer (Figure S4b) films were indexed to bcc crystals with (100) orientation corresponding to space group I4/mmm (#139).

Focused Ion Beam-Scanning Electron Microscopy

After embedding samples in silica, a representative cross-section SEM image of each sample was obtained on a Helios Nanolab 600 dual beam focused ion beam milling system with a 52° relative difference between the ion and electron beam. Scheme S1 shows the cross-section bcc crystallographic orientations obtained by FIB-SEM (Scheme S1). After a layer of titanium was deposited over the area of interest, a 15 μm × 1 μm area, aligned lengthwise with the (100) followed by the (110) plane of the superlattice, was milled with a 93 pA (30 kV) ion beam. Each cross-section was imaged with an 86 pA (5 kV) electron beam using the in-lens detector on the SEM without using the software’s tilt correction. Postimage collection, SEM images of the cross sections were lengthened in the y-direction by the appropriate factor to account for the tilt. Data analysis on cross-sections was done for entire 15 μm cross-section; the larger image was subsequently cropped to a representative section and included in the figures for qualitative reference. The degree of epitaxy was determined using Photoshop and Matlab to track the positions of internal PAEs relative to the positions of the templated posts (Figures S2 and S5).

RMS Roughness and Mean Thickness Calculation

To calculate the thin film thickness and surface root-mean-square (RMS) roughness, the 15 μm cross-section of (100) plane images was cropped into one image, where the posts met the substrate and the topmost PAEs were marked using Photoshop. Mean thickness was measured from the substrate surface to the center of the topmost PAE core and averaged over the entire cross-section (Table S2). Since FIB-SEM images were taken at an angle, the images were adjusted for the tilt using Matlab prior to data processing. RMS roughness was calculated in its standard fashion: RRMS = √(∑(yi2)/N), where N is the number of PAEs on the thin film surface and yi = height-mean height.

Supporting Information

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The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsnano.6b06584.

  • Oligonucleotide sequences, FIB-SEM and SAXS analysis, and additional figures and tables (PDF)

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Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

Author Information

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  • Corresponding Authors
    • Robert J. Macfarlane - Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States;  Email: [email protected]
    • Chad A. Mirkin - †Department of Chemical and Biological Engineering, ‡International Institute for Nanotechnology, §Department of Chemistry, and ⊥Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States;  Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States;  Thomas J. Watson Laboratories of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States;  X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States;  Orcidhttp://orcid.org/0000-0002-6634-7627;  Email: [email protected]
  • Authors
    • Mary X. Wang - †Department of Chemical and Biological Engineering, ‡International Institute for Nanotechnology, §Department of Chemistry, and ⊥Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States;  Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States;  Thomas J. Watson Laboratories of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States;  X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
    • Soyoung E. Seo - †Department of Chemical and Biological Engineering, ‡International Institute for Nanotechnology, §Department of Chemistry, and ⊥Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States;  Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States;  Thomas J. Watson Laboratories of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States;  X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
    • Paul A. Gabrys - Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
    • Dagny Fleischman - Thomas J. Watson Laboratories of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
    • Byeongdu Lee - X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States;  Orcidhttp://orcid.org/0000-0003-2514-8805
    • Youngeun Kim - †Department of Chemical and Biological Engineering, ‡International Institute for Nanotechnology, §Department of Chemistry, and ⊥Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States;  Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States;  Thomas J. Watson Laboratories of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States;  X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
    • Harry A. Atwater - Thomas J. Watson Laboratories of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States;  Orcidhttp://orcid.org/0000-0001-9435-0201
  • Notes
    The authors declare no competing financial interest.

Acknowledgment

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This work was supported by the following awards: AFOSR FA9550-11-1-0275 and FA9550-12-1-0280; the Department of Defense National Security Science and Engineering Faculty Fellowship N00014-15-1-0043; and the Center for Bio-Inspired Energy Science (CBES), an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Basic Energy Sciences under award DE-SC0000989-0002. This work was also supported by the National Science Foundation’s (NSF) MRSEC program (DMR-1121262) and made use of its Shared Facilities at the Materials Research Center of Northwestern University, specifically the EPIC facility of the NUANCE Center, which also receives support from the Soft and Hybrid Nanotechnology Experimental (SHyNE) Resource (NSF NNCI-1542205). X-ray experiments were carried out at beamline 12-ID-B at the Advanced Photon Source (APS), a U.S. DOE Office of Science User Facility operated by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. EBL was performed at the Kavli Nanoscience Institute’s shared instrumentation center. FIB-SEM was performed at the Shared Experimental Facilities supported in part by the MRSEC Program of the NSF (DMR-1419807). M.X.W. acknowledges support from the National Science Foundation Graduate Research Fellowship, a Ryan Fellowship, and the Northwestern University International Institute for Nanotechnology. S.E.S. acknowledges support from the Center for Bio-Inspired Energy Sciences Fellowship and the Northwestern University International Institute for Nanotechnology. Y.K. acknowledges support from a Ryan Fellowship and the Northwestern University International Institute for Nanotechnology.

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    A study aimed at understanding the factors that control the optical properties of DNA-linked gold nanoparticle aggregates contg. oligonucleotide linkers of varying length (24-72 base pairs) is described. In this system, ∼15 nm diam. Au particles modified with (alkanethiol)-12 base oligomers are hybridized to a series of oligonucleotide linkers ranging from 24 to 72 base pairs (∼80-240 Å) in length. Aggregated at room temp., the various macroscopic nanoparticle assemblies have plasmon frequency changes that are inversely dependent on the oligonucleotide linker length. Upon annealing at temps. close to the melting temp. of the DNA, the optical properties of the DNA-linked assemblies contg. the longer linkers (48 and 72 base pairs) red-shift until they are similar to the assemblies contg. the shorter linkers (24 base pairs). The pre- and post-annealed DNA-linked assemblies were characterized by sedimentation rate, transmission electron microscopy, dynamic light scattering, and UV-vis spectroscopy which show that the oligonucleotide linker length kinetically controls the size of the aggregates that are formed under the pre-annealed conditions, thereby controlling the optical properties. Through the use of small-angle X-ray scattering and electrodynamic modeling in conjunction with the techniques mentioned above, we have detd. that the temp.-dependent optical changes obsd. upon annealing of the aggregates contg. the longer oligonucleotides (48 and 72 base pairs) can be attributed to aggregate growth through an "Ostwald ripening" mechanism (where larger aggregates grow at the expense of smaller aggregates). This type of aggregate growth leads to the red-shift in plasmon frequency obsd. for the aggregates. Significantly, these expts. provide evidence that the optical properties of these DNA-linked nanoparticle assemblies are governed by aggregate size, regardless of oligonucleotide linker length, which has important implications for the development of colorimetric detection methods based on these nanoparticle materials.
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    ACS Nano (2016), 10 (2), 1771-1779CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
    A method for modulating the bond strength in DNA-programmable nanoparticle (NP) superlattice crystals utilizes noncovalent interactions between a family of [Ru(dipyrido[2,3-a:3',2'-c]phenazine)(N-N)2]2+-based small mol. intercalators and DNA duplexes to postsynthetically modify DNA-NP superlattices. This increases the strength of the DNA bonds that hold the nanoparticles together, making the superlattices more resistant to thermal degrdn. The authors investigate the relationship between the structure of the intercalator and its binding affinity for DNA duplexes and det. how this translates to the increased thermal stability of the intercalated superlattices. The authors find that intercalator charge and steric profile give us a wide range of tunability and control over DNA-NP bond strength, with the resulting crystal lattices retaining their structure at temps. greater than 50°C above nonintercalated structures. This allows the authors to subject DNA-NP superlattice crystals to conditions under which they would normally melt, enabling the construction of a core-shell (gold NP-quantum dot NP) superlattice crystal.
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    Pal, S.; Zhang, Y.; Kumar, S. K.; Gang, O. Dynamic Tuning of DNA-Nanoparticle Superlattices by Molecular Intercalation of Double Helix J. Am. Chem. Soc. 2015, 137, 4030– 4033 DOI: 10.1021/ja512799d
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    Nanoparticle (NP) assembly using DNA recognition has emerged as a powerful tool for the fabrication of 3D superlattices. In addn. to the vast structural diversity, this approach provides an avenue for dynamic 3D NP assembly, which is promising for the modulation of interparticle distances and, hence, for example, for in situ tuning of optical properties. While several approaches have been explored for changing NP sepns. in the lattices using responsiveness of single-stranded DNA (ss-DNA), far less work has been done for the manipulation of most abundant double-stranded DNA (ds-DNA) motifs. Here, we present a novel strategy for modulation of interparticle distances in DNA linked 3D self-assembled NP lattices by mol. intercalator. We utilize ethidium bromide (EtBr) as a model intercalator to demonstrate selective and isotropic lattice expansion for three superlattice types (bcc, fcc, and AlB2) due to the intercalation of ds-DNA linking NPs. We further show the reversibility of the lattice parameter using n-butanol as a retrieving agent as well as an increased lattice thermal stability by 12-14 °C due to the inclusion of EtBr. The proposed intercalator-based strategy permits the creation of reconfigurable and thermally stable superlattices, which could lead to tunable and functionally responsive materials.
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    Chemistry - A European Journal (2015), 21 (31), 10983-10987CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
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    Auyeung, E.; Macfarlane, R. J.; Choi, C. H. J.; Cutler, J. I.; Mirkin, C. A. Transitioning DNA-Engineered Nanoparticle Superlattices from Solution to the Solid State Adv. Mater. 2012, 24, 5181– 5186 DOI: 10.1002/adma.201202069
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    The authors report a method for stabilizing DNA-assembled three-dimensional superlattices in the solid state by silica encapsulation, where both the symmetries and lattice spacings of the soln.-phase lattices are preserved. Once encapsulated, superlattice morphologies are no longer dictated by DNA interactions, and as such remain stable against distortion, collapse, or dissocn. under many previously inaccessible conditions.
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  • Abstract

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    Scheme 1

    Scheme 1. Layer-by-Layer Assembly of PAE Superlattice Thin Films on a DNA-Functionalized Template
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    Figure 1

    Figure 1. SEM, SAXS, and FIB-SEM characterization of DNA–NP thin films. (a) 2-, 5-, and 10-layer DNA–NP thin films assembled at 25 °C exhibit kinetic roughening and nonepitaxial growth beyond four layers of deposited PAEs. (b) 5- and 10-layer DNA–NP thin films assembled at 25 °C and thermally annealed after the full deposition process demonstrate enhanced ordering, but only the 5-layer sample is fully epitaxial since only PAEs that are close to the initial four epitaxial layers experience sufficient driving force to align with the patterned template. (c) 10-layer DNA–NP thin film where each layer is assembled at an elevated temperature; this process produces smooth, crystalline thin films fully epitaxial with the patterned substrate. Scale bars for SEM and FIB-SEM are 500 and 200 nm, respectively.

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    Figure 2

    Figure 2. Quantitative characterization of films shows that depositing PAEs at near-equilibrium conditions induces (a) higher degree of epitaxy (as determined by SAXS) and (b) more controlled growth and a smoother film morphology (as determined from FIB-SEM).

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    Figure 3

    Figure 3. Optical image of DNA-functionalized NP thin film grown from a template exhibiting an arbitrary geometry. SEM images show that the thin film possesses the same crystallographic orientation across the entire structure.

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  • References

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      A current limitation in nanoparticle superlattice engineering is that the identities of the particles being assembled often det. the structures that can be synthesized. Therefore, specific crystallog. symmetries or lattice parameters can only be achieved using specific nanoparticles as building blocks (and vice versa). The authors present six design rules that can be used to deliberately prep. nine distinct colloidal crystal structures, with control over lattice parameters on the 25- to 150-nm length scale. These design rules outline a strategy to independently adjust each of the relevant crystallog. parameters, including particle size (5 to 60 nm), periodicity, and interparticle distance. As such, this work represents an advance in synthesizing tailorable macroscale architectures comprising nanoscale materials in a predictable fashion.
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      11
      Anisotropic nanoparticle complementarity in DNA-mediated co-crystallization
      O'Brien, Matthew N.; Jones, Matthew R.; Lee, Byeongdu; Mirkin, Chad A.
      Nature Materials (2015), 14 (8), 833-839CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)
      By using DNA as a surface ligand, mixts. of two different anisotropic nanoparticles were selectively cocrystd., and the effects of nanoparticle size and shape complementarity on the resultant crystal symmetry, microstrain, and effective 'DNA bond' length and strength were investigated. These results were used to understand a more complicated system where both size and shape complementarity change, and where one nanoparticle can participate in multiple types of directional interactions. These findings offer improved control of non-spherical nanoparticles as building blocks for the assembly of sophisticated macroscopic materials, and provide a framework to understand complementarity and directional interactions in DNA-mediated nanoparticle crystn.
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      12
      Stepwise Evolution of DNA-Programmable Nanoparticle Superlattices
      Senesi, Andrew J.; Eichelsdoerfer, Daniel J.; Macfarlane, Robert J.; Jones, Matthew R.; Auyeung, Evelyn; Lee, Byeongdu; Mirkin, Chad A.
      Angewandte Chemie, International Edition (2013), 52 (26), 6624-6628CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The authors use a stepwise growth process to systematically study and control the evolution of a bcc. cryst. thin-film comprised of nanoparticle building blocks functionalized with DNA on a complementary DNA substrate. The authors examine crystal growth as a function of temp., no. of layers, and substrate-particle bonding interactions. Importantly, the judicious choice of DNA interconnects allows one to tune the interfacial energy between various crystal planes and the substrate, and thereby control crystal orientation and size in a stepwise fashion using chem. programmable attractive forces.
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      13
      Epitaxial Growth of DNA-Assembled Nanoparticle Superlattices on Patterned Substrates
      Hellstrom, Sondra L.; Kim, Youngeun; Fakonas, James S.; Senesi, Andrew J.; MacFarlane, Robert J.; Mirkin, Chad A.; Atwater, Harry A.
      Nano Letters (2013), 13 (12), 6084-6090CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      Arrays of DNA-functionalized gold nanoparticles have been grown epitaxially on lithog. patterned templates, eliminating grain boundaries and enabling fine control over orientation and size of assemblies up to thousands of square micrometers. This epitaxial growth allowed for orientational control, systematic introduction of strain, and designed defects, which extend the range of structures that can be made using superlattice assembly.
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      Lalander, C. H.; Zheng, Y.; Dhuey, S.; Cabrini, S.; Bach, U. DNA-Directed Self-Assembly of Gold Nanoparticles onto Nanopatterned Surfaces: Controlled Placement of Individual Nanoparticles into Regular Arrays ACS Nano 2010, 4, 6153– 6161 DOI: 10.1021/nn101431k
      14
      DNA-Directed Self-Assembly of Gold Nanoparticles onto Nanopatterned Surfaces: Controlled Placement of Individual Nanoparticles into Regular Arrays
      Lalander, Cecilia H.; Zheng, Yuanhui; Dhuey, Scott; Cabrini, Stefano; Bach, Udo
      ACS Nano (2010), 4 (10), 6153-6161CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      A method for the templated DNA-directed self-assembly of individual gold nanoparticles (AuNPs) into discrete nanostructures is described. The templating nanostructures consisted of a linear configuration of six metal dots with a center-to-center dot distance of 55 nm, fabricated by electron beam lithog. The 40 nm DNA-capped AuNPs were immobilized onto this templating nanostructure to produce a linear configuration of six adjacent AuNPs. The geometry of the templating nanostructure is critically important for the successful direction of a single nanoparticle onto individual adsorption sites. For optimized template structures the immobilization efficiency of nanoparticles onto the individual adsorption sites is 80%. The nonspecific assocn. of nanoparticles with specifically adsorbed nanoparticles and the between adsorption of nanoparticles, bridging two individual adsorption sites, were the two main defects obsd. in the immobilized assemblies. Less than 1% of all surface confined AuNPs adsorbed nonspecifically in the areas between the self-assembled regular arrays.
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      Macfarlane, R. J.; Thaner, R. V.; Brown, K. A.; Zhang, J.; Lee, B.; Nguyen, S. T.; Mirkin, C. A. Importance of the DNA “Bond” in Programmable Nanoparticle Crystallization Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 14995– 15000 DOI: 10.1073/pnas.1416489111
      15
      Importance of the DNA "bond" in programmable nanoparticle crystallization
      MacFarlane, Robert J.; Thaner, Ryan V.; Brown, Keith A.; Zhang, Jian; Lee, Byeongdu; Nguyen, Son Binh T.; Mirkin, Chad A.
      Proceedings of the National Academy of Sciences of the United States of America (2014), 111 (42), 14995-15000CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      If a soln. of DNA-coated nanoparticles is allowed to crystallize, the thermodn. structure can be predicted by a set of structural design rules analogous to Pauling's rules for ionic crystn. The details of the crystn. process, however, have proved more difficult to characterize as they depend on a complex interplay of many factors. Here, we report that this crystn. process is dictated by the individual DNA bonds and that the effect of changing structural or environmental conditions can be understood by considering the effect of these parameters on free oligonucleotides. Specifically, we obsd. the reorganization of nanoparticle superlattices using time-resolved synchrotron small-angle x-ray scattering in systems with different DNA sequences, salt concns., and densities of DNA linkers on the surface of the nanoparticles. The agreement between bulk crystn. and the behavior of free oligonucleotides may bear important consequences for constructing novel classes of crystals and incorporating new interparticle bonds in a rational manner.
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      Zhang, C.; Macfarlane, R. J.; Young, K. L.; Choi, C. H. J.; Hao, L.; Auyeung, E.; Liu, G.; Zhou, X.; Mirkin, C. A. A General Approach to DNA-Programmable Atom Equivalents Nat. Mater. 2013, 12, 741– 746 DOI: 10.1038/nmat3647
      16
      A general approach to DNA-programmable atom equivalents
      Zhang, Chuan; MacFarlane, Robert J.; Young, Kaylie L.; Choi, Chung Hang J.; Hao, Liangliang; Auyeung, Evelyn; Liu, Guoliang; Zhou, Xiaozhu; Mirkin, Chad A.
      Nature Materials (2013), 12 (8), 741-746CODEN: NMAACR; ISSN:1476-1122. (Nature Publishing Group)
      Nanoparticles can be combined with nucleic acids to program the formation of three-dimensional colloidal crystals where the particles' size, shape, compn. and position can be independently controlled. However, the diversity of the types of material that can be used is limited by the lack of a general method for prepg. the basic DNA-functionalized building blocks needed to bond nanoparticles of different chem. compns. into lattices in a controllable manner. By coating nanoparticles protected with aliph. ligands with an azide-bearing amphiphilic polymer, followed by the coupling of DNA to the polymer using strain-promoted azide-alkyne cycloaddn. (also known as copper-free azide-alkyne click chem.), nanoparticles bearing a high-d. shell of nucleic acids can be created regardless of nanoparticle compn. This method provides a route to a virtually endless class of programmable atom equiv. for DNA-based colloidal crystn.
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      Zhang, Y.; Lu, F.; Yager, K. G.; van der Lelie, D.; Gang, O. A General Strategy for the DNA-Mediated Self-Assembly of Functional Nanoparticles into Heterogeneous Systems Nat. Nanotechnol. 2013, 8, 865– 872 DOI: 10.1038/nnano.2013.209
      17
      A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems
      Zhang, Yugang; Lu, Fang; Yager, Kevin G.; van der Lelie, Daniel; Gang, Oleg
      Nature Nanotechnology (2013), 8 (11), 865-872CODEN: NNAABX; ISSN:1748-3387. (Nature Publishing Group)
      Nanoparticles coated with DNA mols. can be programmed to self-assemble into three-dimensional superlattices. Such superlattices can be made from nanoparticles with different functionalities and could potentially exploit the synergetic properties of the nanoscale components. However, the approach has so far been used primarily with single-component systems. Here, the authors report a general strategy for the creation of heterogeneous nanoparticle superlattices using DNA and carboxylic-based conjugation. Nanoparticles with all major types of functionality-plasmonic (gold), magnetic (Fe2O3), catalytic (palladium) and luminescent (CdSe/Te@ZnS and CdS@ZnS)-can be incorporated into binary systems in a rational manner. The authors also examine the effect of nanoparticle characteristics (including size, shape, no. of DNA per particle and DNA flexibility) on the phase behavior of the heterosystems, and demonstrate that the assembled materials can have novel optical and field-responsive properties.
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    18. 18
      Lee, J.-S.; Lytton-Jean, A. K.; Hurst, S. J.; Mirkin, C. A. Silver Nanoparticle-Oligonucleotide Conjugates Based on DNA with Triple Cyclic Disulfide Moieties Nano Lett. 2007, 7, 2112– 2115 DOI: 10.1021/nl071108g
      18
      Silver Nanoparticle-Oligonucleotide Conjugates Based on DNA with Triple Cyclic Disulfide Moieties
      Lee, Jae-Seung; Lytton-Jean, Abigail K. R.; Hurst, Sarah J.; Mirkin, Chad A.
      Nano Letters (2007), 7 (7), 2112-2115CODEN: NALEFD; ISSN:1530-6984. (American Chemical Society)
      The authors report a new strategy for prepg. silver nanoparticle-oligonucleotide conjugates that are based upon DNA with cyclic disulfide-anchoring groups. These particles are extremely stable and can withstand NaCl concns. up to 1.0 M. When silver nanoparticles functionalized with complementary sequences are combined, they assemble to form DNA-linked nanoparticle networks. This assembly process is reversible with heating and is assocd. with a red shifting of the particle surface plasmon resonance and a concomitant color change from yellow to pale red. Analogous to the oligonucleotide-functionalized gold nanoparticles, these particles also exhibit highly cooperative binding properties with extremely sharp melting transitions. This work is an important step toward using silver nanoparticle-oligonucleotide conjugates for a variety of purposes, including mol. diagnostic labels, synthons in programmable materials synthesis approaches, and functional components for nanoelectronic and plasmonic devices.
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    19. 19
      Brodin, J. D.; Auyeung, E.; Mirkin, C. A. DNA-Mediated Engineering of Multicomponent Enzyme Crystals Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 4564– 4569 DOI: 10.1073/pnas.1503533112
      19
      DNA-mediated engineering of multicomponent enzyme crystals
      Brodin, Jeffrey D.; Auyeung, Evelyn; Mirkin, Chad A.
      Proceedings of the National Academy of Sciences of the United States of America (2015), 112 (15), 4564-4569CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)
      The ability to predictably control the coassembly of multiple nanoscale building blocks, esp. those with disparate chem. and phys. properties such as biomols. and inorg. nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is esp. true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, the authors explore the concept of trading protein-protein interactions for DNA-DNA interactions to direct the assembly of two nucleic-acid-functionalized proteins with distinct surface chemistries into six unique lattices composed of catalytically active proteins, or of a combination of proteins and DNA-modified gold nanoparticles. The programmable nature of DNA-DNA interactions used in this strategy allows the authors to control the lattice symmetries and unit cell consts., as well as the compns. and habit, of the resulting crystals. This study provides a potentially generalizable strategy for constructing a unique class of materials that take advantage of the diverse morphologies, surface chemistries, and functionalities of proteins for assembling functional cryst. materials.
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    20. 20
      Evanoff, D. D.; Chumanov, G. Synthesis and Optical Properties of Silver Nanoparticles and Arrays ChemPhysChem 2005, 6, 1221– 1231 DOI: 10.1002/cphc.200500113
      20
      Synthesis and optical properties of silver nanoparticles and arrays
      Evanoff, David D., Jr.; Chumanov, George
      ChemPhysChem (2005), 6 (7), 1221-1231CODEN: CPCHFT; ISSN:1439-4235. (Wiley-VCH Verlag GmbH & Co. KGaA)
      A review. This Minireview systematically examines optical properties of Ag nanoparticles as a function of size. Extinction, scattering, and absorption cross sections and distance dependence of the local electromagnetic field, as well as the quadrupolar coupling of 2-dimensional assemblies of such particles are exptl. measured for a wide range of particle sizes. Such measurements were possible because of the development of a novel synthetic method for the size-controlled synthesis of chem. clean, highly cryst. Ag nanoparticles of narrow size distribution. The method and its unique advantages are compared to other methods for synthesis of metal nanoparticles. Synthesis and properties of nanocomposite materials using these and other nanoparticles are also described. Important highlights in the history of the field of metal nanoparticles as well as an examn. of the basic principles of plasmon resonances are included.
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    21. 21
      Kelly, K. L.; Coronado, E.; Zhao, L. L.; Schatz, G. C. The Optical Properties of Metal Nanoparticles: The Influence of Size, Shape, and Dielectric Environment J. Phys. Chem. B 2003, 107, 668– 677 DOI: 10.1021/jp026731y
      21
      The Optical Properties of Metal Nanoparticles: The Influence of Size, Shape, and Dielectric Environment
      Kelly, K. Lance; Coronado, Eduardo; Zhao, Lin Lin; Schatz, George C.
      Journal of Physical Chemistry B (2003), 107 (3), 668-677CODEN: JPCBFK; ISSN:1520-6106. (American Chemical Society)
      The optical properties of metal nanoparticles have long been of interest in phys. chem., starting with Faraday's studies of colloidal Au in the middle 1800s. More recently, new lithog. techniques as well as improvements to classical wet chem. methods have made it possible to synthesize noble metal nanoparticles with a wide range of sizes, shapes, and dielec. environments. In this feature article, the authors describe recent progress in the theory of nanoparticle optical properties, particularly methods for solving Maxwell's equations for light scattering from particles of arbitrary shape in a complex environment. Included is a description of the qual. features of dipole and quadrupole plasmon resonances for spherical particles; a discussion of anal. and numerical methods for calcg. extinction and scattering cross sections, local fields, and other optical properties for nonspherical particles; and a survey of applications to problems of recent interest involving triangular Ag particles and related shapes.
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    22. 22
      Storhoff, J. J.; Lazarides, A. A.; Mucic, R. C.; Mirkin, C. A.; Letsinger, R. L.; Schatz, G. C. What Controls the Optical Properties of DNA-Linked Gold Nanoparticle Assemblies? J. Am. Chem. Soc. 2000, 122, 4640– 4650 DOI: 10.1021/ja993825l
      22
      What Controls the Optical Properties of DNA-Linked Gold Nanoparticle Assemblies?
      Storhoff, James J.; Lazarides, Anne A.; Mucic, Robert C.; Mirkin, Chad A.; Letsinger, Robert L.; Schatz, George C.
      Journal of the American Chemical Society (2000), 122 (19), 4640-4650CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      A study aimed at understanding the factors that control the optical properties of DNA-linked gold nanoparticle aggregates contg. oligonucleotide linkers of varying length (24-72 base pairs) is described. In this system, ∼15 nm diam. Au particles modified with (alkanethiol)-12 base oligomers are hybridized to a series of oligonucleotide linkers ranging from 24 to 72 base pairs (∼80-240 Å) in length. Aggregated at room temp., the various macroscopic nanoparticle assemblies have plasmon frequency changes that are inversely dependent on the oligonucleotide linker length. Upon annealing at temps. close to the melting temp. of the DNA, the optical properties of the DNA-linked assemblies contg. the longer linkers (48 and 72 base pairs) red-shift until they are similar to the assemblies contg. the shorter linkers (24 base pairs). The pre- and post-annealed DNA-linked assemblies were characterized by sedimentation rate, transmission electron microscopy, dynamic light scattering, and UV-vis spectroscopy which show that the oligonucleotide linker length kinetically controls the size of the aggregates that are formed under the pre-annealed conditions, thereby controlling the optical properties. Through the use of small-angle X-ray scattering and electrodynamic modeling in conjunction with the techniques mentioned above, we have detd. that the temp.-dependent optical changes obsd. upon annealing of the aggregates contg. the longer oligonucleotides (48 and 72 base pairs) can be attributed to aggregate growth through an "Ostwald ripening" mechanism (where larger aggregates grow at the expense of smaller aggregates). This type of aggregate growth leads to the red-shift in plasmon frequency obsd. for the aggregates. Significantly, these expts. provide evidence that the optical properties of these DNA-linked nanoparticle assemblies are governed by aggregate size, regardless of oligonucleotide linker length, which has important implications for the development of colorimetric detection methods based on these nanoparticle materials.
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    23. 23
      Choi, J.-H.; Wang, H.; Oh, S. J.; Paik, T.; Sung, P.; Sung, J.; Ye, X.; Zhao, T.; Diroll, B. T.; Murray, C. B. Exploiting the Colloidal Nanocrystal Library to Construct Electronic Devices Science 2016, 352, 205– 208 DOI: 10.1126/science.aad0371
      23
      Exploiting the colloidal nanocrystal library to construct electronic devices
      Choi, Ji-Hyuk; Wang, Han; Oh, Soong Ju; Paik, Taejong; Sung, Pil; Sung, Jinwoo; Ye, Xingchen; Zhao, Tianshuo; Diroll, Benjamin T.; Murray, Christopher B.; Kagan, Cherie R.
      Science (Washington, DC, United States) (2016), 352 (6282), 205-208CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      Synthetic methods produce libraries of colloidal nanocrystals with tunable phys. properties by tailoring the nanocrystal size, shape, and compn. Here, the authors exploit colloidal nanocrystal diversity and design the materials, interfaces, and processes to construct all-nanocrystal electronic devices using soln.-based processes. Metallic silver and semiconducting cadmium selenide nanocrystals are deposited to form high-cond. and high-mobility thin-film electrodes and channel layers of field-effect transistors. Insulating aluminum oxide nanocrystals are assembled layer by layer with polyelectrolytes to form high-dielec. const. gate insulator layers for low-voltage device operation. Metallic indium nanocrystals are codispersed with silver nanocrystals to integrate an indium supply in the deposited electrodes that serves to passivate and dope the cadmium selenide nanocrystal channel layer. The authors fabricate all-nanocrystal field-effect transistors on flexible plastics with electron mobilities of 21.7 square centimeters per V-second.
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    24. 24
      Jonsson, P. E. Superparamagnetism and Spin Glass Dynamics of Interacting Magnetic Nanoparticle Systems Adv. Chem. Phys. 2003, 128, 191– 248 DOI: 10.1002/0471484237.ch3
      There is no corresponding record for this reference.
    25. 25
      Li, T.; Senesi, A. J.; Lee, B. Small Angle X-Ray Scattering for Nanoparticle Research Chem. Rev. 2016, 116, 11128 DOI: 10.1021/acs.chemrev.5b00690
      25
      Small Angle X-ray Scattering for Nanoparticle Research
      Li, Tao; Senesi, Andrew J.; Lee, Byeongdu
      Chemical Reviews (Washington, DC, United States) (2016), 116 (18), 11128-11180CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      X-ray scattering is a structural characterization tool that has impacted diverse fields of study. It is unique in its ability to examine materials in real time and under realistic sample environments, enabling researchers to understand morphol. at nanometer and angstrom length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), resp. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theor. foundation for X-ray scattering, considering both form factor and structure factor, as well as the use of correlation functions, which may be used to det. a particle's size, size distribution, shape, and organization into hierarchical structures. The theory is expanded upon with contemporary use cases. Both transmission and reflection (grazing incidence) geometries are addressed, as well as the combination of SAXS with other X-ray and non-X-ray characterization tools. We conclude with an examn. of several key areas of research where X-ray scattering has played a pivotal role, including in situ nanoparticle synthesis, nanoparticle assembly, and operando studies of catalysts and energy storage materials. Throughout this review we highlight the unique capabilities of X-ray scattering for structural characterization of materials in their native environment.
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    26. 26
      Meyers, S. T.; Anderson, J. T.; Hung, C. M.; Thompson, J.; Wager, J. F.; Keszler, D. A. Aqueous Inorganic Inks for Low-Temperature Fabrication of ZnO TFTs J. Am. Chem. Soc. 2008, 130, 17603– 17609 DOI: 10.1021/ja808243k
      26
      Aqueous Inorganic Inks for Low-Temperature Fabrication of ZnO TFTs
      Meyers, Stephen T.; Anderson, Jeremy T.; Hung, Celia M.; Thompson, John; Wager, John F.; Keszler, Douglas A.
      Journal of the American Chemical Society (2008), 130 (51), 17603-17609CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      A simple, low-cost, and nontoxic aq. ink chem. is described for digital printing of ZnO films. Selective design through controlled pptn., purifn., and dissoln. affords an aq. Zn(OH)x(NH3)y(2-x)+ soln. that is stable in storage, yet promptly decomps. at temps. <150° to form wurtzite ZnO. Dense, high-quality, polycryst. ZnO films are deposited by ink-jet printing and spin-coating, and film structure is elucidated via x-ray diffraction and electron microscopy. Semiconductor film functionality and quality were examd. through integration in bottom-gate thin-film transistors. Enhancement-mode TFTs with ink-jet printed ZnO channels annealed at 300° exhibit strong field effect and excellent current satn. in tandem with incremental mobilities from 4-6 cm2 V-1 s-1. Spin-coated ZnO semiconductors processed at 150° are integrated with soln.-deposited aluminum oxide phosphate dielecs. in functional transistors, demonstrating both high performance, i.e., mobilities up to 1.8 cm2 V-1 s-1, and the potential for low-temp. soln. processing of all-oxide electronics.
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    27. 27
      Seo, S. E.; Wang, M. X.; Shade, C. M.; Rouge, J. L.; Brown, K. A.; Mirkin, C. A. Modulating the Bond Strength of DNA–Nanoparticle Superlattices ACS Nano 2016, 10, 1771– 1779 DOI: 10.1021/acsnano.5b07103
      27
      Modulating the Bond Strength of DNA-Nanoparticle Superlattices
      Seo, Soyoung E.; Wang, Mary X.; Shade, Chad M.; Rouge, Jessica L.; Brown, Keith A.; Mirkin, Chad A.
      ACS Nano (2016), 10 (2), 1771-1779CODEN: ANCAC3; ISSN:1936-0851. (American Chemical Society)
      A method for modulating the bond strength in DNA-programmable nanoparticle (NP) superlattice crystals utilizes noncovalent interactions between a family of [Ru(dipyrido[2,3-a:3',2'-c]phenazine)(N-N)2]2+-based small mol. intercalators and DNA duplexes to postsynthetically modify DNA-NP superlattices. This increases the strength of the DNA bonds that hold the nanoparticles together, making the superlattices more resistant to thermal degrdn. The authors investigate the relationship between the structure of the intercalator and its binding affinity for DNA duplexes and det. how this translates to the increased thermal stability of the intercalated superlattices. The authors find that intercalator charge and steric profile give us a wide range of tunability and control over DNA-NP bond strength, with the resulting crystal lattices retaining their structure at temps. greater than 50°C above nonintercalated structures. This allows the authors to subject DNA-NP superlattice crystals to conditions under which they would normally melt, enabling the construction of a core-shell (gold NP-quantum dot NP) superlattice crystal.
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    28. 28
      Pal, S.; Zhang, Y.; Kumar, S. K.; Gang, O. Dynamic Tuning of DNA-Nanoparticle Superlattices by Molecular Intercalation of Double Helix J. Am. Chem. Soc. 2015, 137, 4030– 4033 DOI: 10.1021/ja512799d
      28
      Dynamic tuning of DNA-nanoparticle superlattices by molecular intercalation of double helix
      Pal, Suchetan; Zhang, Yugang; Kumar, Sanat K.; Gang, Oleg
      Journal of the American Chemical Society (2015), 137 (12), 4030-4033CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Nanoparticle (NP) assembly using DNA recognition has emerged as a powerful tool for the fabrication of 3D superlattices. In addn. to the vast structural diversity, this approach provides an avenue for dynamic 3D NP assembly, which is promising for the modulation of interparticle distances and, hence, for example, for in situ tuning of optical properties. While several approaches have been explored for changing NP sepns. in the lattices using responsiveness of single-stranded DNA (ss-DNA), far less work has been done for the manipulation of most abundant double-stranded DNA (ds-DNA) motifs. Here, we present a novel strategy for modulation of interparticle distances in DNA linked 3D self-assembled NP lattices by mol. intercalator. We utilize ethidium bromide (EtBr) as a model intercalator to demonstrate selective and isotropic lattice expansion for three superlattice types (bcc, fcc, and AlB2) due to the intercalation of ds-DNA linking NPs. We further show the reversibility of the lattice parameter using n-butanol as a retrieving agent as well as an increased lattice thermal stability by 12-14 °C due to the inclusion of EtBr. The proposed intercalator-based strategy permits the creation of reconfigurable and thermally stable superlattices, which could lead to tunable and functionally responsive materials.
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    29. 29
      Shade, C. M.; Kennedy, R. D.; Rouge, J. L.; Rosen, M. S.; Wang, M. X.; Seo, S. E.; Clingerman, D. J.; Mirkin, C. A. Duplex-Selective Ruthenium-Based DNA Intercalators Chem. - Eur. J. 2015, 21, 10983– 10987 DOI: 10.1002/chem.201502095
      29
      Duplex-Selective Ruthenium-Based DNA Intercalators
      Shade, Chad M.; Kennedy, Robert D.; Rouge, Jessica L.; Rosen, Mari S.; Wang, Mary X.; Seo, Soyoung E.; Clingerman, Daniel J.; Mirkin, Chad A.
      Chemistry - A European Journal (2015), 21 (31), 10983-10987CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)
      We report the design and synthesis of small mols. that exhibit enhanced luminescence in the presence of duplex rather than single-stranded DNA. The local environment presented by a well-known [Ru(dipyrido[3,2-a:2',3'-c]phenazine)L2]2+-based DNA intercalator was modified by functionalizing the bipyridine ligands with esters and carboxylic acids. By systematically varying the no. and charge of the pendant groups, it was detd. that decreasing the electrostatic interaction between the intercalator and the anionic DNA backbone reduced single-strand interactions and translated to better duplex specificity. In studying this class of complexes, a single RuII complex emerged that selectively luminesces in the presence of duplex DNA with little to no background from interacting with single-stranded DNA. This complex shows promise as a new dye capable of selectively staining double- vs. single-stranded DNA in gel electrophoresis, which cannot be done with conventional SYBR dyes.
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    30. 30
      Auyeung, E.; Macfarlane, R. J.; Choi, C. H. J.; Cutler, J. I.; Mirkin, C. A. Transitioning DNA-Engineered Nanoparticle Superlattices from Solution to the Solid State Adv. Mater. 2012, 24, 5181– 5186 DOI: 10.1002/adma.201202069
      30
      Transitioning DNA-Engineered Nanoparticle Superlattices from Solution to the Solid State
      Auyeung, Evelyn; MacFarlane, Robert J.; Choi, Chung Hang J.; Cutler, Joshua I.; Mirkin, Chad A.
      Advanced Materials (Weinheim, Germany) (2012), 24 (38), 5181-5186, S5181/1-S5181/12CODEN: ADVMEW; ISSN:0935-9648. (Wiley-VCH Verlag GmbH & Co. KGaA)
      The authors report a method for stabilizing DNA-assembled three-dimensional superlattices in the solid state by silica encapsulation, where both the symmetries and lattice spacings of the soln.-phase lattices are preserved. Once encapsulated, superlattice morphologies are no longer dictated by DNA interactions, and as such remain stable against distortion, collapse, or dissocn. under many previously inaccessible conditions.
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    • Oligonucleotide sequences, FIB-SEM and SAXS analysis, and additional figures and tables (PDF)


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