The Role of Repulsion in Colloidal Crystal Engineering with DNA.

Hybridization interactions between DNA-functionalized nanoparticles (DNA-NPs) can be used to program the crystallization behavior of superlattices, yielding access to complex three-dimensional structures with more than 30 different lattice symmetries. The first superlattice structures using DNA-NPs as building blocks were identified almost a decade ago, yet the role of repulsive interactions in guiding structure formation is still largely unexplored. Here, a comprehensive approach is taken to study the role of repulsion in the assembly behavior of DNA-NPs, enabling the calculation of interparticle interaction potentials based on experimental results. In this work, we used two different means to assemble DNA-NPs-Watson-Crick base-pairing interactions and depletion interactions-and systematically varied the salt concentration to study the effective interactions in DNA-NP superlattices. A comparison between the two systems allows us to decouple the repulsive forces from the attractive hybridization interactions that are sensitive to the ionic environment. We find that the gap distance between adjacent DNA-NPs follows a simple power law dependence on solution ionic strength regardless of the type of attractive forces present. This result suggests that the observed trend is driven by repulsive interactions. To better understand such behavior, we propose a mean-field model that provides a mathematical description for the observed trend. This model shows that the trend is due to the variation in the effective cross-sectional diameter of DNA duplex and the thickness of DNA shell.

Small Angle X-ray Scattering for Nanoparticle Research.

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 morphology at nanometer and angstrom length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), respectively. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theoretical 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 determine 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 examination 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.

Oligonucleotide flexibility dictates crystal quality in DNA-programmable nanoparticle superlattices.

The evolution of crystallite size and microstrain in DNA-mediated nanoparticle superlattices is dictated by annealing temperature and the flexibility of the interparticle bonds. This work addresses a major challenge in synthesizing optical metamaterials based upon noble metal nanoparticles by enabling the crystallization of large nanoparticles (100 nm diameter) at high volume fractions (34% metal).

Reconstitutable nanoparticle superlattices.

Colloidal self-assembly predominantly results in lattices that are either: (1) fixed in the solid state and not amenable to additional modification, or (2) in solution, capable of dynamic adjustment, but difficult to transition to other environments. Accordingly, approaches to both dynamically adjust the interparticle spacing of nanoparticle superlattices and reversibly transfer superlattices between solution-phase and solid state environments are limited. In this manuscript, we report the reversible contraction and expansion of nanoparticles within immobilized monolayers, surface-assembled superlattices, and free-standing single crystal superlattices through dehydration and subsequent rehydration. Interestingly, DNA contraction upon dehydration occurs in a highly uniform manner, which allows access to spacings as small as 4.6 nm and as much as a 63% contraction in the volume of the lattice. This enables one to deliberately control interparticle spacings over a 4-46 nm range and to preserve solution-phase lattice symmetry in the solid state. This approach could be of use in the study of distance-dependent properties of nanoparticle superlattices and for long-term superlattice preservation.

DNA-mediated nanoparticle crystallization into Wulff polyhedra.

Crystallization is a fundamental and ubiquitous process much studied over the centuries. But although the crystallization of atoms is fairly well understood, it remains challenging to predict reliably the outcome of molecular crystallization processes that are complicated by various molecular interactions and solvent involvement. This difficulty also applies to nanoparticles: high-quality three-dimensional crystals are mostly produced using drying and sedimentation techniques that are often impossible to rationalize and control to give a desired crystal symmetry, lattice spacing and habit (crystal shape). In principle, DNA-mediated assembly of nanoparticles offers an ideal opportunity for studying nanoparticle crystallization: a well-defined set of rules have been developed to target desired lattice symmetries and lattice constants, and the occurrence of features such as grain boundaries and twinning in DNA superlattices and traditional crystals comprised of molecular or atomic building blocks suggests that similar principles govern their crystallization. But the presence of charged biomolecules, interparticle spacings of tens of nanometres, and the realization so far of only polycrystalline DNA-interconnected nanoparticle superlattices, all suggest that DNA-guided crystallization may differ from traditional crystal growth. Here we show that very slow cooling, over several days, of solutions of complementary-DNA-modified nanoparticles through the melting temperature of the system gives the thermodynamic product with a specific and uniform crystal habit. We find that our nanoparticle assemblies have the Wulff equilibrium crystal structure that is predicted from theoretical considerations and molecular dynamics simulations, thus establishing that DNA hybridization can direct nanoparticle assembly along a pathway that mimics atomic crystallization.

Epitaxial growth of DNA-assembled nanoparticle superlattices on patterned substrates.

DNA-functionalized nanoparticles, including plasmonic nanoparticles, can be assembled into a wide range of crystalline arrays via synthetically programmable DNA hybridization interactions. Here we demonstrate that such assemblies can be grown epitaxially on lithographically patterned templates, eliminating grain boundaries and enabling fine control over orientation and size of assemblies up to thousands of square micrometers. We also demonstrate that this epitaxial growth allows for orientational control, systematic introduction of strain, and designed defects, which extend the range of structures that can be made using superlattice assembly. Ultimately, this will open the door to integrating self-assembled plasmonic nanoparticle materials into on-chip optical or optoelectronic platforms.

One-dimensional nanorod arrays: independent control of composition, length, and interparticle spacing with nanometer precision.

We report the synthesis of solution dispersible, one-dimensional metal nanostructure arrays as small as 35 nm in diameter using on-wire lithography, wherein feature thickness and spacing in the arrays is tailorable down to approximately 6 and 1 nm, respectively. Using this unique level of control, we present solution-averaged extinction spectra of 35 nm diameter Au nanorod dimers with varying gap sizes to illustrate the effect of gap size on plasmon coupling between nanorods. Additionally, we demonstrate control over the composition of the arrays with Au, Ni, and Pt segments, representing important advances in controlling the ordering of sub-100 nm nanostructures that are not available with current synthesis or assembly methods.

DNA-nanoparticle superlattices formed from anisotropic building blocks.

Directional bonding interactions in solid-state atomic lattices dictate the unique symmetries of atomic crystals, resulting in a diverse and complex assortment of three-dimensional structures that exhibit a wide variety of material properties. Methods to create analogous nanoparticle superlattices are beginning to be realized, but the concept of anisotropy is still largely underdeveloped in most particle assembly schemes. Some examples provide interesting methods to take advantage of anisotropic effects, but most are able to make only small clusters or lattices that are limited in crystallinity and especially in lattice parameter programmability. Anisotropic nanoparticles can be used to impart directional bonding interactions on the nanoscale, both through face-selective functionalization of the particle with recognition elements to introduce the concept of valency, and through anisotropic interactions resulting from particle shape. In this work, we examine the concept of inherent shape-directed crystallization in the context of DNA-mediated nanoparticle assembly. Importantly, we show how the anisotropy of these particles can be used to synthesize one-, two- and three-dimensional structures that cannot be made through the assembly of spherical particles.

Agarose-assisted dip-pen nanolithography of oligonucleotides and proteins.

This paper describes a method for the direct transfer of biomolecules encapsulated within a viscous fluid matrix by dip-pen nanolithography (DPN). The method relies on the use of agarose as a "universal" carrier that is compatible with many types of biomolecules including proteins and oligonucleotides. Agarose-assisted DPN allows one to generate nanoarrays of such materials on activated glass substrates with the same deposition rates for different biomolecules, which will greatly expand future capabilities for parallel, multiplexed biomolecule deposition. The fluidity of the matrix may be systematically varied to control the deposition process, resulting in an additional parameter affecting deposition rates besides tip-substrate contact-time and humidity. Agarose-assisted DPN results in extremely fast biomolecule patterning with typical contact times less than 1 s. Feature sizes as small as 50 nm are demonstrated. The biorecognition properties of both protein and oligonucleotide structures are characterized by studying their reactivity with fluorophore-labeled antibody and complementary oligonucleotide sequences, respectively.

Molecular recognition and self-assembly special feature: Assembly and organization processes in DNA-directed colloidal crystallization.

We present an analysis of the key steps involved in the DNA-directed assembly of nanoparticles into crystallites and polycrystalline aggregates. Additionally, the rate of crystal growth as a function of increased DNA linker length, solution temperature, and self-complementary versus non-self-complementary DNA linker strands (1- versus 2-component systems) has been studied. The data show that the crystals grow via a 3-step process: an initial "random binding" phase resulting in disordered DNA-AuNP aggregates, followed by localized reorganization and subsequent growth of crystalline domain size, where the resulting crystals are well-ordered at all subsequent stages of growth.

Redox-activating dip-pen nanolithography (RA-DPN).

Dip pen nanolithography (DPN) involves the direct transfer of an ink from a coated atomic force microscope (AFM) tip to a substrate of interest and uses as many as 55,000 pens to form arbitrary patterns of alkanethiols, oligonucleotides, proteins, and viruses. Two limitations of DPN are the difficulty in transporting high molecular weight inks and the need to optimize individually the transport rates and tip inking methods of each molecule. As an alternative strategy that circumvents these two challenges, a method termed redox activating DPN (RA-DPN) is reported. In this strategy, an electrochemically active, quinone functionalized surface is toggled from the reduced hydroquinone form to the oxidized benzoquinone form by the delivery of an oxidant by DPN. While the benzoquinone form is susceptible to nucleophilic attack in Michael-type additions, hydroquinone is not and acts as a passivating agent. Because both forms of the quinone are kinetically stable, the patterned surface can be immersed in a solution of a target containing any strong nucleophile, which will react only where the benzoquinone form persists on the surface. For proof-of-concept demonstrations, quinone surfaces were patterned by the delivery of the oxidant cerric ammonium nitrate and were immersed in solutions of AF549 labeled cholera toxin beta subunit or oligonucleotides modified at the 5' end with an amine and the 3' end with a fluorophore. Fluorescent patterns of both the proteins and oligonucleotides were observed by epifluorescence microscopy. Additionally, RA-DPN maintains the advantageous ability of DPN to control feature size by varying the dwell time of the tip on the surface, and variation of this parameter has resulted in feature sizes as small as 165 nm. With this resolution, patterns of 50,000 spots could be made in a 100 x 100 microm(2) grid.

Controlling the lattice parameters of gold nanoparticle FCC crystals with duplex DNA linkers.

DNA-functionalized gold nanoparticles can be used to induce the formation and control the unit cell parameters of highly ordered face-centered cubic crystal lattices. Nanoparticle spacing increases linearly with longer DNA interconnect length, yielding maximum unit cell parameters of 77 nm and 0.52% inorganic-filled space for the DNA constructs studied. In general, we show that longer DNA connections result in a decrease in the overall crystallinity and order of the lattice due to greater conformational flexibility.