Aptamers as Functional Modules for DNA Nanostructures.

Watson-Crick base-pairing of DNA allows the nanoscale fabrication of biocompatible synthetic nanostructures for diagnostic and therapeutic biomedical purposes. DNA nanostructure design elicits exquisite control of shape and conformation compared to other nanoparticles. Furthermore, nucleic acid aptamers can be coupled to DNA nanostructures to allow interaction and response to a plethora of biomolecules beyond nucleic acids. When compared to the better-known approach of using protein antibodies for molecular recognition, nucleic acid aptamers are bespoke with the underlying DNA nanostructure backbone and have various other stability, synthesis, and cost advantages. Here, we provide detailed methodologies to synthesize and characterize aptamer-enabled DNA nanostructures. The methods described can be generally applied to various designs of aptamer-enabled DNA nanostructures with a wide range of applications both within and beyond biomedical nanotechnology.

Patterning of supported gold monolayers via chemical lift-off lithography.

The supported monolayer of Au that accompanies alkanethiolate molecules removed by polymer stamps during chemical lift-off lithography is a scarcely studied hybrid material. We show that these Au-alkanethiolate layers on poly(dimethylsiloxane) (PDMS) are transparent, functional, hybrid interfaces that can be patterned over nanometer, micrometer, and millimeter length scales. Unlike other ultrathin Au films and nanoparticles, lifted-off Au-alkanethiolate thin films lack a measurable optical signature. We therefore devised fabrication, characterization, and simulation strategies by which to interrogate the nanoscale structure, chemical functionality, stoichiometry, and spectral signature of the supported Au-thiolate layers. The patterning of these layers laterally encodes their functionality, as demonstrated by a fluorescence-based approach that relies on dye-labeled complementary DNA hybridization. Supported thin Au films can be patterned via features on PDMS stamps (controlled contact), using patterned Au substrates prior to lift-off (e.g., selective wet etching), or by patterning alkanethiols on Au substrates to be reactive in selected regions but not others (controlled reactivity). In all cases, the regions containing Au-alkanethiolate layers have a sub-nanometer apparent height, which was found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure.

Polymer-Pen Chemical Lift-Off Lithography.

We designed and fabricated large arrays of polymer pens having sub-20 nm tips to perform chemical lift-off lithography (CLL). As such, we developed a hybrid patterning strategy called polymer-pen chemical lift-off lithography (PPCLL). We demonstrated PPCLL patterning using pyramidal and v-shaped polymer-pen arrays. Associated simulations revealed a nanometer-scale quadratic relationship between contact line widths of the polymer pens and two other variables: polymer-pen base line widths and vertical compression distances. We devised a stamp support system consisting of interspersed arrays of flat-tipped polymer pens that are taller than all other sharp-tipped polymer pens. These supports partially or fully offset stamp weights thereby also serving as a leveling system. We investigated a series of v-shaped polymer pens with known height differences to control relative vertical positions of each polymer pen precisely at the sub-20 nm scale mimicking a high-precision scanning stage. In doing so, we obtained linear-array patterns of alkanethiols with sub-50 nm to sub-500 nm line widths and minimum sub-20 nm line width tunable increments. The CLL pattern line widths were in agreement with those predicted by simulations. Our results suggest that through informed design of a stamp support system and tuning of polymer-pen base widths, throughput can be increased by eliminating the need for a scanning stage system in PPCLL without sacrificing precision. To demonstrate functional microarrays patterned by PPCLL, we inserted probe DNA into PPCLL patterns and observed hybridization by complementary target sequences.

Plasmonic polymers unraveled through single particle spectroscopy.

Plasmonic polymers are quasi one-dimensional assemblies of nanoparticles whose optical responses are governed by near-field coupling of localized surface plasmons. Through single particle extinction spectroscopy correlated with electron microscopy, we reveal the effect of the composition of the repeat unit, the chain length, and extent of disorder on the energies, intensities, and line shapes of the collective resonances of individual plasmonic polymers constructed from three different sizes of gold nanoparticles. Our combined experimental and theoretical analysis focuses on the superradiant plasmon mode, which results from the most attractive interactions along the nanoparticle chain and yields the lowest energy resonance in the spectrum. This superradiant mode redshifts with increasing chain length until an infinite chain limit, where additional increases in chain length cause negligible change in the energy of the superradiant mode. We find that, among plasmonic polymers of equal width comprising nanoparticles with different sizes, the onset of the infinite chain limit and its associated energy are dictated by the number of repeat units and not the overall length of the polymer. The intensities and linewidths of the superradiant mode relative to higher energy resonances, however, differ as the size and number of nanoparticles are varied in the plasmonic polymers studied here. These findings provide general guidelines for engineering the energies, intensities, and line shapes of the collective optical response of plasmonic polymers constructed from nanoparticles with sizes ranging from a few tens to one hundred nanometers.

Turning the corner: efficient energy transfer in bent plasmonic nanoparticle chain waveguides.

For integrating and multiplexing of subwavelength plasmonic waveguides with other optical and electric components, complex architectures such as junctions with sharp turns are necessary. However, in addition to intrinsic losses, bending losses severely limit plasmon propagation. In the current work, we demonstrate that propagation of surface plasmon polaritons around 90° turns in silver nanoparticle chains occurs without bending losses. Using a far-field fluorescence method, bleach-imaged plasmon propagation (BlIPP), which creates a permanent map of the plasmonic near-field through bleaching of a fluorophore coated on top of a plasmonic waveguide, we measured propagation lengths at 633 nm for straight and bent silver nanoparticle chains of 8.0 ± 0.5 and 7.8 ± 0.4 µm, respectively. These propagation lengths were independent of the input polarization. We furthermore show that subradiant plasmon modes yield a longer propagation length compared to energy transport via excitation of super-radiant modes.

Toward plasmonic polymers.

We establish the concept of a plasmonic polymer, whose collective optical properties depend on the repeat unit. Experimental and theoretical analyses of the super- and sub- radiant plasmon response of plasmonic polymers comprising repeat units of single nanoparticles or dimers of gold nanoparticles show that (1) the redshift of the lowest energy coupled mode becomes minimal as the chain approaches the infinite chain limit at a length of ∼10 particles, (2) the presence and energy of the modes are sensitive to the geometries of the constituents, that is, repeat unit, but (3) spatial disorder and nanoparticle heterogeneity have only small effects on the super-radiant mode.

Radiative and nonradiative properties of single plasmonic nanoparticles and their assemblies.

A surface plasmon is the coherent oscillation of the conduction band electrons. When a metal nanoparticle is excited to produce surface plasmons, incident light is both scattered and absorbed, giving rise to brilliant colors. One available technique for measuring these processes, ensemble extinction spectroscopy, only measures the sum of scattering and absorption. Although the spectral responses of these processes are closely related, their relative efficiencies can differ significantly as a function of nanoparticle size and shape. For some applications, researchers may need techniques that can quantitatively measure absorption or scattering alone. Through advances in single particle spectroscopy, researchers can overcome this problem, separately determining the radiative (elastic and inelastic scattering) and nonradiative (absorption) properties of surface plasmons. Furthermore, because we can use the same sample preparation for both single particle spectroscopy measurements and electron microscopy, this technique provides detailed structural information and a direct correlation between optical properties and nanostructure morphology. In this Account, we present our quantitative investigations of both radiative (scattering and one-photon luminescence) and nonradiative (absorption) properties of the same individual plasmonic nanostructures employing different single particle spectroscopy techniques. In particular, we have used a combined setup to study the same structure with dark-field scattering spectroscopy, photothermal heterodyne imaging, confocal luminescence microscopy, and scanning electron microscopy. While Mie theory thoroughly describes the overall size dependence of scattering and absorption for nanospheres, our real samples deviate significantly from the predicted trend: their particle shape is not perfectly spherical, especially when supported on a substrate. Because of the high excitation rate in laser based single particle measurements, we can efficiently detect one-photon luminescence despite a low quantum yield. For gold nanoparticles, the luminescence spectrum follows the scattering response, and therefore we assigned it to the emission of a plasmon. Due to strong near-field interactions the plasmonic response of closely spaced nanoparticles deviates significantly from that of the constituent nanoparticles. This response arises from coupled surface plasmon modes that combine those of the individual nanoparticles. Our correlated structural and optical imaging strategy is especially powerful for understanding these collective modes and their dependence on the assembly geometry.

Electromagnetic energy transport in nanoparticle chains via dark plasmon modes.

Using light to exchange information offers large bandwidths and high speeds, but the miniaturization of optical components is limited by diffraction. Converting light into electron waves in metals allows one to overcome this problem. However, metals are lossy at optical frequencies and large-area fabrication of nanometer-sized structures by conventional top-down methods can be cost-prohibitive. We show electromagnetic energy transport with gold nanoparticles that were assembled into close-packed linear chains. The small interparticle distances enabled strong electromagnetic coupling causing the formation of low-loss subradiant plasmons, which facilitated energy propagation over many micrometers. Electrodynamic calculations confirmed the dark nature of the propagating mode and showed that disorder in the nanoparticle arrangement enhances energy transport, demonstrating the viability of using bottom-up nanoparticle assemblies for ultracompact opto-electronic devices.

Low absorption losses of strongly coupled surface plasmons in nanoparticle assemblies.

Coupled surface plasmons in one-dimensional assemblies of metal nanoparticles have attracted significant attention because strong interparticle interactions lead to large electromagnetic field enhancements that can be exploited for localizing and amplifying electromagnetic radiation in nanoscale structures. Ohmic loss (i.e., absorption by the metal), however, limits the performance of any application due to nonradiative surface plasmon relaxation. While absorption losses have been studied theoretically, they have not been quantified experimentally for strongly coupled surface plasmons. Here, we report on the ohmic loss in one-dimensional assemblies of gold nanoparticles with small interparticle separations of only a few nanometers and hence strong plasmon coupling. Both the absorption and scattering cross-sections of coupled surface plasmons were determined and compared to electrodynamic simulations. A lower absorption and higher scattering cross-section for coupled surface plasmons compared to surface plasmons of isolated nanoparticles suggest that coupled surface plasmons suffer smaller ohmic losses and therefore act as better antennas. These experimental results provide important insight for the design of plasmonic devices.

Seeing double: coupling between substrate image charges and collective plasmon modes in self-assembled nanoparticle superstructures.

The interaction between adjacent metal nanoparticles within an assembly induces interesting collective plasmonic properties. Using dark-field imaging of plasmon scattering, we investigated rings of gold nanoparticles and observed that the images were dependent on the substrate. In particular, for nanoparticles assembled on carbon and gold substrates, intensity line sections perpendicular to the ring revealed a significant broadening beyond the optical resolution accompanied by an intensity dip in the middle of the line profile. Overall, this appeared in the image as a "splitting" into two offset circles along the direction of the scattered light polarization. This effect was not observed for a substrate with a low permittivity, such as glass. By varying the substrate as well as selecting different detected wavelengths and polarization components of the excitation light, we were able to confirm that the observed effect was due to coupling of collective plasmon modes with their induced image charges in the supporting substrates. These results suggest that plasmon scattering in extended nanostructures can be spatially modulated by tuning the permittivity of the substrate.

Effects of symmetry breaking and conductive contact on the plasmon coupling in gold nanorod dimers.

We have explored the consequences of symmetry breaking on the coupled surface plasmon resonances in individual dimers of gold nanorods using single-particle dark-field scattering spectroscopy and numerical simulations. Pairs of chemically grown nanorods can exhibit wide variation in sizes, gap distances, and relative orientation angles. The combination of single-particle spectroscopy and theoretical analysis allowed us to discern the effects of specific asymmetry-inducing parameters one at a time. The dominant influence of symmetry breaking occurred for longitudinal resonances in strongly coupled nanorods in linear end-to-end configurations. In particular, we found that the normally dark antibonding dimer mode becomes visible when the sizes of the two nanorods are different. In addition, we observed a conductively coupled plasmon mode that was red-shifted by at least 250 nm from the bonding plasmon mode for the corresponding nontouching geometry. Gaining detailed insight into how symmetry breaking influences coupled surface plasmon resonances of individual nanorod dimers is an important step toward the general understanding of the optical properties of assemblies of chemically synthesized nanorods with unavoidable irregularities in size and orientation.

Plasmonic nanorod absorbers as orientation sensors.

Nanoparticles are actively exploited as biological imaging probes. Of particular interest are gold nanoparticles because of their nonblinking and nonbleaching absorption and scattering properties that arise from the excitation of surface plasmons. Nanoparticles with anisotropic shapes furthermore provide information about the probe orientation and its environment. Here we show how the orientation of single gold nanorods (25 x 73 nm) can be determined from both the transverse and longitudinal surface plasmon resonance by using polarization-sensitive photothermal imaging. By measuring the orientation of the same nanorods separately using scanning electron microscopy, we verified the high accuracy of this plasmon-absorption-based technique. However, care had to be taken when exciting the transverse plasmon absorption using a large numerical aperture objective as out-of-plane plasmon oscillations were also excited then. For the size regime studied here, being able to establish the nanorod orientation from the transverse mode is unique to photothermal imaging and almost impossible with conventional dark-field scattering spectroscopy. This is important because the transverse surface plasmon resonance is mostly insensitive to the medium refractive index and nanorod aspect ratio allowing nanorods of any length to be used as orientation sensors without changing the laser frequency.

One-dimensional coupling of gold nanoparticle plasmons in self-assembled ring superstructures.

Plasmon coupling in ordered metal nanoparticle assemblies leads to tunable collective surface plasmon resonances that strongly depend on the interparticle distance. Here we report on the surface plasmon scattering of polystyrene-functionalized 40 nm gold nanoparticles self-assembled into close-packed rings. Using single particle dark-field scattering spectroscopy, we observed strong near-field coupling between neighboring nanoparticles, which results in red-shifted multipolar plasmon modes highly polarized along the ring circumference. Correlated optical spectroscopy and scanning electron microscopy of individual rings with different diameters revealed that the plasmon coupling is independent of ring curvature and mostly insensitive to the local nanoparticle arrangement. Our results further suggest that a one-dimensional gold nanoparticle assembly yields long-range collective plasmonic properties similar to those of metallic nanowires.

Ordered mesoporous materials from metal nanoparticle-block copolymer self-assembly.

The synthesis of ordered mesoporous metal composites and ordered mesoporous metals is a challenge because metals have high surface energies that favor low surface areas. We present results from the self-assembly of block copolymers with ligand-stabilized platinum nanoparticles, leading to lamellar CCM-Pt-4 and inverse hexagonal (CCM-Pt-6) hybrid mesostructures with high nanoparticle loadings. Pyrolysis of the CCM-Pt-6 hybrid produces an ordered mesoporous platinum-carbon nanocomposite with open and large pores (>/=10 nanometers). Removal of the carbon leads to ordered porous platinum mesostructures. The platinum-carbon nanocomposite has very high electrical conductivity (400 siemens per centimeter) for an ordered mesoporous material fabricated from block copolymer self-assembly.

Generalized route to metal nanoparticles with liquid behavior.

We report the generalized synthesis of metal nanoparticles with liquid-like behavior. We introduce a thiol-containing ionic liquid, N,N-dioctyl-N-(3-mercaptopropyl)-N-methylammonium bromide, which serves as a ligand for platinum, gold, palladium, and rhodium nanoparticles. A rapid reduction using THF-soluble metal salts in the presence of the thiol generates nanoparticles with tunable sizes and size distributions. The as-synthesized nanoparticles are a solid and decompose before melting. Upon exchange of the halide anion for an amphiphilic sulfonate anion, however, the nanoparticles exhibit liquid-like properties at room temperature. The liquids have high metal loadings; for example, the 2.7 nm platinum nanoparticle liquid is 36% platinum by mass.