DNA-Functionalized, Bivalent Proteins

Bivalent DNA conjugates of β-galactosidase (βGal), having pairs of oligonucleotides positioned closely on opposing faces of the protein, have been synthesized and characterized. These structures, due to their directional bonding characteristics, allow for the programmable access of one-dimensional protein materials. When conjugates functionalized with complementary oligonucleotides are combined under conditions that support DNA hybridization, periodic wire-type superstructures consisting of aligned proteins form. These structures have been characterized by gel electrophoresis, cryo-transmission electron microscopy, and negative-stain transmission electron microscopy. Significantly, melting experiments of complementary building blocks display narrowed and elevated melting transitions compared to the free duplex DNA, further supporting the formation of the designed binding mode, and unambiguously characterizing their association as DNA-mediated. These novel structures illustrate, for the first time, that directional DNA bonding can be realized with only a pair of DNA modifications, which will allow one to engineer directional interactions and realize new classes of superstructures not possible simply through shape control or isotropically functionalized materials

Spherical Nucleic Acids

A historical perspective of the development of spherical nucleic acid (SNA) conjugates and other three-dimensional nucleic acid nanostructures is provided. This Perspective details the synthetic methods for preparing them, followed by a discussion of their unique properties and theoretical and experimental models for understanding them. Important examples of technological advances made possible by their fundamental properties spanning the fields of chemistry, molecular diagnostics, gene regulation, medicine, and materials science are also presented

Dynamically Interchangeable Nanoparticle Superlattices Through the Use of Nucleic Acid-Based Allosteric Effectors

DNA is a powerful tool for programmably assembling colloidal crystals, and has been used to generate nanoparticle superlattices with synthetically adjustable lattice parameters and crystal symmetries. However, the majority of these superlattice structures remain static once constructed, and factors such as interparticle distance cannot be controlled in a facile and rapid manner. Incorporation of these materials into functional devices would be greatly benefitted by the ability to change various aspects of the crystal assembly after the lattice has been synthesized. Herein, we present a reversible, rapid, and stoichiometric on-the-fly manipulation of nanoparticle superlattices with allosteric effectors based upon DNA. This approach is applicable to multiple different crystal symmetries, including FCC, BCC, CsCl, and AlB₂

Infinite Coordination Polymer Particles Composed of Stimuli-Responsive Coordination Complex Subunits

Infinite Coordination Polymer Particles Composed of Stimuli-Responsive Coordination Complex Subunit

Nanopatterned Extracellular Matrices Enable Cell-Based Assays with a Mass Spectrometric Readout

Cell-based assays are finding wider use in evaluating compounds in primary screens for drug development, yet it is still challenging to measure enzymatic activities as an end point in a cell-based assay. This paper reports a strategy that combines state-of-the-art cantilever free polymer pen lithography (PPL) with self-assembled monolayer laser desorption–ionization (SAMDI) mass spectrometry to guide cell localization and measure cellular enzymatic activities. Experiments are conducted with a 384 spot array, in which each spot is composed of ∼400 nanoarrays and each array has a 10 × 10 arrangement of 750 nm features that present extracellular matrix (ECM) proteins surrounded by an immobilized phosphopeptide. Cells attach to the individual nanoarrays, where they can be cultured and treated with small molecules, after which the media is removed and the cells are lysed. Phosphatase enzymes in the proximal lysate can then act on the immobilized phosphopeptide substrate to convert it to the dephosphorylated form. After the lysate is removed, the array is analyzed by SAMDI mass spectrometry to identify the extent of dephosphorylation and, therefore, the amount of enzyme activity in the cell. This novel approach of using nanopatterning to mediate cell adhesion and SAMDI to record enzyme activities in the proximal lysate will enable a broad range of cellular assays for applications in drug discovery and research not possible with conventional strategies

Critical Undercooling in DNA-Mediated Nanoparticle Crystallization

The nucleation of DNA-functionalized nanoparticle superlattices is observed to exhibit a temperature hysteresis between melting (superlattice dissociation) and freezing (particle association) transitions that allows for the study of nucleation thermodynamics. Through detailed study of the assembly of these particles, which can be considered programmable atom equivalents (PAEs), we identify this hysteresis as critical undercoolinga phase transition phenomenon related to a thermodynamic barrier to nucleation. The separable nature of the DNA bonding elements and nanoparticle core enables the PAE platform to pose unique questions about the microscopic dependencies of critical undercooling and, ultimately, to control the nucleation pathway. Specifically, we find that the undercooling required to initiate nucleation increases as the nanoparticle coordination number increases (number of particles to which a single particle can bind)

Optical Properties of One‑, Two‑, and Three-Dimensional Arrays of Plasmonic Nanostructures

This Feature Article describes research on the optical properties of arrays of silver and gold nanoparticles, particles that exhibit localized surface plasmon resonances in the visible and near-infrared. These resonances lead to strong absorption and scattering of light that is strongly dependent on nanoparticle size and shape. When arranged into multidimensional arrays, the nanoparticles strongly interact such that the collective properties can be rationally designed by changing the dimensions of the array (one-, two-, or three-dimensional), interparticle spacing, and array shape or morphology. Emerging from this work is a large body of literature focusing on one-, two-, and three-dimensional arrays, which provide unique opportunities for realizing materials with interesting and unusual photonic and metamaterial properties. Electrodynamics theory provides an accurate description of the optical properties, often based on simple models such as coupled dipoles, effective medium theory, and anomalous diffraction. In turn, simple models and simulation methods allow for the prediction and explanation of a variety of observed optical properties. In one and two dimensions, these tunable optical properties range from extinction spectra that are red- or blue-shifted compared to the isolated particles to lattice plasmon modes that involve strong interactions between localized plasmon resonances in the nanoparticles and photonic modes that derive from Bragg diffraction in the crystalline array. Three-dimensional arrays can exhibit unique effective medium properties, such as negative permittivity that leads to metallic optical response even when there is less than 1% metal content in the array. They also can be rationally designed to have photonic scattering modes dictated and controlled by interactions between nanoscale plasmonic nanoparticles and the mesoscale superlattice crystal habit (i.e., the crystalline size, shape, and morphology). This discussion of plasmonic arrays across multiple dimensions provides a comprehensive description of those factors that can be easily tuned for the design of plasmon-based optical materials

Small Molecule Regulation of Self-Association and Catalytic Activity in a Supramolecular Coordination Complex

Herein, we report the synthesis and characterization of the first weak-link approach (WLA) supramolecular construct that employs the small molecule regulation of intermolecular hydrogen bonding interactions for the in situ control of catalytic activity. A biaryl urea group, prone to self-aggregation, was functionalized with a phosphinoalkyl thioether (P,S) hemilabile moiety and incorporated into a homoligated Pt­(II) tweezer WLA complex. This urea-containing construct, which has been characterized by a single crystal X-ray diffraction study, can be switched in situ from a rigid fully closed state to a flexible semiopen state via Cl^– induced changes in the coordination mode at the Pt­(II) structural node. FT-IR and ¹H NMR spectroscopy studies were used to demonstrate that while extensive urea self-association persists in the flexible semiopen complex, these interactions are deterred in the rigid, fully closed complex because of geometric and steric restraints. Consequently, the urea moieties in the fully closed complex are able to catalyze a Diels-Alder reaction between cyclopentadiene and methyl vinyl ketone to generate 2-acetyl-5-norbornene. The free urea ligand and the semiopen complex show no such activity. The successful incorporation and regulation of a hydrogen bond donating catalyst in a WLA construct open the doors to a vast and rapidly growing catalogue of allosteric catalysts for applications in the detection and amplification of organic analytes

Fast Charge Extraction in Perovskite-Based Core–Shell Nanowires

Realizing nanostructured interfaces with precise architectural control enables one to access properties unattainable using bulk materials. In particular, a nanostructured interface (<i>e</i>.<i>g</i>., a core–shell nanowire) between two semiconductors leads to a short charge separation distance, such that photoexcited charge carriers can be more quickly and efficiently collected. While vapor-phase growth methods are used to synthesize uniform core–shell nanowire arrays of semiconductors such as Si and InP, more general strategies are required to produce related structures composed of a broader range of materials. Herein, we employ anodic aluminum oxide templates to synthesize CH₃NH₃PbI₃ perovskite core–copper thiocyanate shell nanowire arrays employing a combination of electrodeposition and solution casting methods. Using scanning electron microscopy, powder X-ray diffraction, and time-resolved photoluminescence spectroscopy, we confirm the target structure and show that adopting a core–shell nanowire architecture accelerates the rate of charge quenching by nearly 3 orders of magnitude compared to samples with only an axial junction. Subsequently, we fit decay curves to a triexponential function to attribute fast quenching in core–shell nanowires to charge extraction by the copper thiocyanate nanotubes, as opposed to recombination within the perovskite nanowires. Dramatic improvements to charge extraction speed and efficiency result from the substantially reduced charge separation distance and increased interfacial area achieved <i>via</i> the core–shell nanowire array architecture

CRISPR Spherical Nucleic Acids

The use of CRISPR/Cas9 systems in genome editing has been limited by the inability to efficiently deliver the key editing components to and across tissues and cell membranes, respectively. Spherical nucleic acids (SNAs) are nanostructures that provide privileged access to both but have yet to be explored as a means of facilitating gene editing. Herein, a new class of CRISPR SNAs are designed and evaluated in the context of genome editing. Specifically, Cas9 ProSNAs comprised of Cas9 cores densely modified with DNA on their exteriors and preloaded with single-guide RNA were synthesized and evaluated for their genome editing capabilities in the context of multiple cell lines. The radial orientation of the DNA on the Cas9 protein surface enhances cellular uptake, without the need for electroporation or transfection agents. In addition, the Cas9 proteins defining the cores of the ProSNAs were fused with GALA peptides on their N-termini and nuclear localization signals on their C-termini to facilitate endosomal escape and maximize nuclear localization and editing efficiency, respectively. These constructs were stable against protease digestion under conditions that fully degrade the Cas9 protein, when not transformed into an SNA, and used to achieve genome editing efficiency between 32 and 47%. Taken together, these novel constructs and advances point toward a way of significantly broadening the scope of use and impact of CRISPR-Cas9 genome editing systems