Impact of the Core Chemistry of Self-Assembled Spherical Nucleic Acids on their In Vitro Fate.

Nucleic acid therapeutics (NATs), such as mRNA, small interfering RNA or antisense oligonucleotides are extremely efficient tools to modulate gene expression and tackle otherwise undruggable diseases. Spherical nucleic acids (SNAs) can efficiently deliver small NATs to cells while protecting their payload from nucleases, and have improved biodistribution and muted immune activation. Self-assembled SNAs have emerged as nanostructures made from a single DNA-polymer conjugate with similar favorable properties as well as small molecule encapsulation. However, because they maintain their structure by non-covalent interactions, they might suffer from disassembly in biologically relevant conditions, especially with regard to their interaction with serum proteins. Here, we report a systematic study of the factors that govern the fate of self-assembled SNAs. Varying the core chemistry and using stimuli-responsive disulfide crosslinking, we show that extracellular stability upon binding with serum proteins is important for recognition by membrane receptors, triggering cellular uptake. At the same time, intracellular dissociation is required for efficient therapeutic release. Disulfide-crosslinked SNAs combine these two properties and result in efficient and non-toxic unaided gene silencing therapeutics. We anticipate these investigations will help the translation of promising self-assembled structures towards in vivo gene silencing applications.

Minimalist Design of Wireframe DNA Nanotubes: Tunable Geometry, Size, Chirality, and Dynamics.

DNA nanotubes (NTs) have attracted extensive interest as artificial cytoskeletons for biomedical, synthetic biology, and materials applications. Here, we report the modular design and assembly of a minimalist yet robust DNA wireframe nanotube with tunable cross-sectional geometry, cavity size, chirality, and length, while using only four DNA strands. We introduce an h-motif structure incorporating double-crossover (DX) tile-like DNA edges to achieve structural rigidity and provide efficient self-assembly of h-motif-based DNA nanotube (H-NT) units, thus producing programmable, micrometer-long nanotubes. We demonstrate control of the H-NT nanotube length via short DNA modulators. Finally, we use an enzyme, RNase H, to take these structures out of equilibrium and trigger nanotube assembly at a physiologically relevant temperature, underlining future cellular applications. The minimalist H-NTs can assemble at near-physiological salt conditions and will serve as an easily synthesized, DNA-economical modular template for biosensors, plasmonics, or other functional materials and as cost-efficient drug-delivery vehicles for biomedical applications.

Programming rigidity into size-defined wireframe DNA nanotubes.

Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and in vivo biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes. Subtle design changes govern the structure and properties of our nanotubes, which are built from a custom-made, long, and size-defined template strand to which DNA rungs and linkers are attached. Unlike DNA origami, these custom-made strands possess regions with repeating sequences at strategic locations, thereby reducing the number of strands necessary for assembly. Through strand displacement, the nanotubes can be reversibly altered between extended and collapsed morphologies. These design concepts enable fine-tuning of the nanotube stiffness and may pave the way for the development of designer nanotubes for a variety of applications, including the study of cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.

Small Molecule-Templated DNA Hydrogel with Record Stiffness Integrates and Releases DNA Nanostructures and Gene Silencing Nucleic Acids.

Deoxyribonucleic acid (DNA) hydrogels are a unique class of programmable, biocompatible materials able to respond to complex stimuli, making them valuable in drug delivery, analyte detection, cell growth, and shape-memory materials. However, unmodified DNA hydrogels in the literature are very soft, rarely reaching a storage modulus of 103  Pa, and they lack functionality, limiting their applications. Here, a DNA/small-molecule motif to create stiff hydrogels from unmodified DNA, reaching 105  Pa in storage modulus is used. The motif consists of an interaction between polyadenine and cyanuric acid-which has 3-thymine like faces-into multimicrometer supramolecular fibers. The mechanical properties of these hydrogels are readily tuned, they are self-healing and thixotropic. They integrate a high density of small, nontoxic molecules, and are functionalized simply by varying the molecule sidechain. They respond to three independent stimuli, including a small molecule stimulus. These stimuli are used to integrate and release DNA wireframe and DNA origami nanostructures within the hydrogel. The hydrogel is applied as an injectable delivery vector, releasing an antisense oligonucleotide in cells, and increasing its gene silencing efficacy. This work provides tunable, stimuli-responsive, exceptionally stiff all-DNA hydrogels from simple sequences, extending these materials' capabilities.

Stabilization of Functional DNA Structures with Mild Photochemical Methods.

A significant barrier to biological applications of DNA structures is their instability to nucleases. UV-mediated thymine dimerization can crosslink and stabilize DNA nanostructures, but its effect on DNA strand hybridization fidelity and function is unclear. In this work, we first compare a number of methods for DNA irradiation with different wavelengths of light and different photosensitizers. We demonstrate that all approaches can achieve nuclease protection; however, the levels of DNA off-target crosslinking and damage vary. We then describe mild irradiation conditions intended to safeguard DNA against nuclease degradation. We demonstrate up to 25× increase in serum stability while minimizing off-target damage and maintaining functions such as hybridization efficiency, gene silencing, aptamer binding, and DNA nanostructure formation. Our methodology requires no complex instruments beyond a UV light source and no synthetic modification of the DNA itself, allowing for applications in numerous areas of nucleic acid therapy and nanotechnology.

Asymmetric patterning drives the folding of a tripodal DNA nanotweezer.

DNA tweezers have emerged as powerful devices for a wide range of biochemical and sensing applications; however, most DNA tweezers consist of single units activated by DNA recognition, limiting their range of motion and ability to respond to complex stimuli. Herein, we present an extended, tripodal DNA nanotweezer with a small molecule junction. Simultaneous, asymmetric elongation of our molecular core is achieved using polymerase chain reaction (PCR) to produce length- and sequence-specific DNA arms with repeating DNA regions. When rigidified, our DNA tweezer can be addressed with streptavidin-binding ligands. Full control over the number, separation, and location of these ligands enables site-specific streptavidin recognition; all three arms of the DNA nanotweezer wrap around multiple streptavidin units simultaneously. Our approach combines the simplicity of DNA tile arrays with the size regime normally provided by DNA origami, offering an integrated platform for the use of branched DNA scaffolds as structural building blocks, protein sensors, and dynamic, stimuli-responsive materials.

Amplified Self-Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA-Minimal Architectures.

Triggering the release of small molecules in response to unique biomarkers is important for applications in drug delivery and biodetection. Due to low quantities of biomarker, amplifying release is necessary to gain appreciable responses. Nucleic acids have been used for both their biomarker-recognition properties and as stimuli, notably in amplified small-molecule release by nucleic-acid-templated catalysis (NATC). The multiple components and reversibility of NATC, however, make it difficult to apply in vivo. Herein, we report the use of the hybridization chain reaction (HCR) for the amplified, conditional release of small molecules from standalone nanodevices. We couple HCR with a DNA-templated reaction resulting in the amplified, immolative release of small molecules. We integrate the HCR components into single nanodevices as DNA tracks and spherical nucleic acids, spatially isolating reactive groups until triggering. This could be applied to biosensing, imaging, and drug delivery.

Tuning the structural properties of cadmium-aluminum layered double hydroxide for enhanced photocatalytic dye degradation.

The distinctive layered structure, chemical stability and tunability of layered double hydroxides (LDHs) have led to extensive investigations in various areas of photocatalysis, including photocatalytic water splitting, carbon dioxide photoreduction, and degradation of organic pollutants. Here, a series of visible light active cadmium-aluminum layered double hydroxides (CdAl LDHs) with various Cd2+ : Al3+ ratios is synthesized via the reaction-diffusion framework (RDF) leading thereby to a hierarchal spherical structure of the LDH. The aim of this study is to develop an optimal CdAl LDH photocatalyst that is activated by solar light irradiation and tested for methylene blue (MB) degradation. The structural and physicochemical properties of the synthesized materials are determined by several imaging and spectroscopic techniques. The photocatalytic study reveals a strong dependence of the photocatalytic activity of the CdAl LDH on the cationic ratio with an optimal performance at a ratio Cd2+ : Al3+ equal to 3 : 1. A mechanism is proposed whereby the activity is ascribed to the formation of intermediate reactive oxidative species (ROS) during the photodegradation reactions and scrutinised by invoking different ROS quenchers and corroborated by density functional theory (DFT) calculations.

The global diabetes epidemic and the nonprofit state corporate complex: Equity implications of discourses, research agendas, and policy recommendations of diabetes nonprofit organizations.

Important insights have been gained from studying how corporate social actors -- such as Big Tobacco or Big Food -- influence how global health issues are framed, debated, and addressed, and in so doing contribute to reproducing health inequities. Less attention has been paid to the role of nonprofit organizations (NPOs), even when all too often NPOs actively contribute to these inequities through normalizing discourses and practices that legitimize establishment views, poor public policies and existing relations of power. Our study attempts to fill this gap by assessing the influence on global health inequities of major NPOs -- specifically three disease associations -- whose mission includes preventing type 2 diabetes (henceforth diabetes) or reducing inequities in the global diabetes epidemic. No longer considered a "disease of prosperity", diabetes is known to affect the poor and racialized minorities disproportionately, in countries at all levels of income. While the contribution of the social and political determinants of health is well established, major NPOs ostensibly committed to eradicate, or at least moderate the effects of, diabetes give short shrift to these determinants, framing them at best as the context that promotes behaviours that combine with genetic predispositions to drive the inequitable, global distribution of diabetes. Drawing from Marxian theory and critical discourse analysis, we assess publicly available information - on educational and policy prescriptions, funding sources, corporate affiliations, funded research and social media presence -- pertaining to one Canadian, one US and one international NPO to identify discourses and practices that may contribute to the global, unequal distribution of diabetes and elaborate on their implications for health equity more broadly.

"Printing" DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence.

The incorporation of synthetic molecules as corner units in DNA structures has been of interest over the last two decades. In this work, we present a facile method for generating branched small molecule-DNA hybrids with controllable valency, different sequences, and directionalities (5'-3') using a "printing" process from a simple 3-way junction structure. We also show that the DNA-imprinted small molecule can be extended asymmetrically using polymerase chain reaction (PCR) and can be replicated chemically. This strategy provides opportunities to achieve new structural motifs in DNA nanotechnology and introduce new functionalities to DNA nanostructures.

Crystal Growth of ZIF-8, ZIF-67, and Their Mixed-Metal Derivatives.

A facile method to produce zeolitic imidazolate frameworks (ZIF-8, ZIF-67, and solid-solution ZIFs (mixed Co and Zn)) is reported. ZIF crystals are produced via a reaction-diffusion framework (RDF) by diffusing an outer solution at a relatively high concentration of the 2-methyl imidazole linker (HmIm) into an agar gel matrix containing the metal ions (zinc(II) and/or cobalt(II)) at room temperature. Accordingly, a propagating supersaturation wave, initiated at the interface between the outer solution and the gel matrix, leads to a precipitation front with a gradient of crystal sizes ranging between 100 nm and 55 µm along the reaction tube. While the precipitation fronts of ZIF-8 and ZIF-67 travel the same distance for the same initial conditions, ZIF-8 crystals therein are consistently smaller than the ZIF-67 crystals due to the disparity of their rate of nucleation and growth. The effects of the temperature, the concentration of the reagents, and the thickness of the gel matrix on the growth of the ZIF crystals are investigated. We also show that by using RDF we can envisage the formation mechanism of the ZIF crystals, which consists of the aggregation of ZIF nanospheres to form the ZIF-8 dodecahedrons. Moreover, using RDF, the formation of a solid-solution ZIF via the incorporation of Co(II) and Zn(II) cations within the same framework is achieved in a controlled manner. Finally, we demonstrate that doping ZIF-8 by Co(II) enhances the photodegradation of methylene blue dye under visible light irradiation in the absence of hydrogen peroxide.

Kinetics of intercalation of fluorescent probes in magnesium-aluminium layered double hydroxide within a multiscale reaction-diffusion framework.

We report the synthesis of magnesium-aluminium layered double hydroxide (LDH) using a reaction-diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium-aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Cadmium-Aluminum Layered Double Hydroxide Microspheres for Photocatalytic CO2 Reduction.

We report the synthesis of cadmium-aluminum layered double hydroxide (CdAl LDH) using the reaction-diffusion framework. As the hydroxide anions diffuse into an agar gel matrix containing the mixture of aluminum and cadmium salts at a given ratio, they react to give the LDH. The LDH self-assembles inside the pores of the gel matrix into a unique spherical-porous shaped microstructure. The internal and external morphologies of the particles are studied by electron microscopy and tomography revealing interconnected channels and a high surface area. This material is shown to exhibit a promising performance in the photoreduction of carbon dioxide using solar light. Moreover, the palladium-decorated version shows a significant improvement in its reduction potential at room temperature.