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.

Two-Dimensional Supramolecular Polymerization of DNA Amphiphiles is Driven by Sequence-Dependent DNA-Chromophore Interactions.

Two-dimensional (2D) assemblies of water-soluble block copolymers have been limited by a dearth of systematic studies that relate polymer structure to pathway mechanism and supramolecular morphology. Here, we employ sequence-defined triblock DNA amphiphiles for the supramolecular polymerization of free-standing DNA nanosheets in water. Our systematic modulation of amphiphile sequence shows the alkyl chain core forming a cell membrane-like structure and the distal π-stacking chromophore block folding back to interact with the hydrophilic DNA block on the nanosheet surface. This interaction is crucial to sheet formation, marked by a chiral "signature", and sensitive to DNA sequence, where nanosheets form with a mixed sequence, but not with a homogeneous poly(thymine) sequence. This work opens the possibility of forming well-ordered, bilayer-like assemblies using a single DNA amphiphile for applications in cell sensing, nucleic acid therapeutic delivery and enzyme arrays.

Lyotropic Nematic Phases of Isotropic Nanoparticles via Semiflexible Polymer Ligands.

Lyotropic liquid crystalline (LC) nanomaterials are normally achieved through particle shape anisotropy. Herein, it is shown that lyotropic nematic rather than cubic phases are produced from spherical nanoparticles (NPs) with semi-flexible polymer ligands. ZrO2 nanocrystals (4 nm dia.) are coated with a dense shell of poly(hexyl isocyanate) (PHIC), a helical rod-like polymer that forms lyotropic LC phases in a range of organic solvents. Solvent casted NPs with PHIC ligands above the persistence length form linear assemblies, separated by a characteristic distance related to the chain length while NPs with shorter, rigid rod PHIC ligands pack hexagonally. Concentrated NP-PHIC dispersions present nematic textures similar to the free PHIC nematic solutions but at lower critical concentrations, widening the isotropic-nematic biphasic region. 2 H NMR spectra of the NPs dispersed in a deuterated solvent display quadrupolar splittings that increase with NP concentration, showing that the PHIC ligands are magnetically aligned. The high degree of orientation order is evidence that splaying of the ligand shell transforms the spherical NPs to rod-like shapes that assemble to produce nematic lyotropic LC phases and linear NP arrays. This approach to creating anisotropic assemblies can be extended to other types of spherical NPs and semiflexible polymers.

Ligand-flexible synthesis of strongly confined perovskite nanocrystals: a microwave synthetic approach.

Perovskite nanocrystals (PNCs) and their strongly confined versions have traditionally been synthesized via hot injection methods. However, there is a pressing need for a new synthesis method that offers more flexible surface chemistry, improved optical properties, and greater sample stability. Here we explore and exploit the recently introduced microwave (MW) synthesis method, focusing on temperature and coating ligands, including a polymer ligand for which the hot injection method is unsuitable. The optimized microwave synthetic protocols produce PNCs with better exciton definition, lower polydispersity, and stronger ligand attachment than their hot injection counterparts. A variety of characterization techniques were employed to compare the properties of PNCs produced by the hot injection versus microwave methods. Insight into the molecular basis for the improved PNC properties was provided by FTIR and several NMR experiments that revealed the nature of the attachment of different ligands and their interactions with the PNCs. The overall results demonstrate that MW synthesis is a promising alternative to the HI method, particularly if smaller PNCs with strong quantum confinement are desired.

Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics.

Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.

Polymer Functionalized Nanoparticles in Blue Phase LC: Effect of Particle Shape.

Ethylene oxide oligomers and polymers, free and tethered to gold nanoparticles, were dispersed in blue phase liquid crystals (BPLC). Gold nanospheres (AuNPs) and nanorods (AuNRs) were functionalized with thiolated ethylene oxide ligands with molecular weights ranging from 200 to 5000 g/mol. The BPLC mixture (ΔTBP ~6 °C) was based on the mesogenic acid heterodimers, n-hexylbenzoic acid (6BA) and n-trans-butylcyclohexylcarboxylic acid (4-BCHA) with the chiral dopant (R)-2-octyl 4-[4-(hexyloxy)benzoyloxy]benzoate. The lowest molecular weight oligomer lowered and widened the BP range but adding AuNPs functionalized with the same ligand had little effect. Higher concentrations or molecular weights of the ligands, free or tethered to the AuNPs, completely destabilized the BP. Mini-AuNRs functionalized with the same ligands lowered and widened the BP temperature range with longer mini-AuNRs having a larger effect. In contrast to the AuNPs, the mini-AuNRs with the higher molecular weight ligands widened rather than destabilized the BP, though the lowest MW ligand yielded the largest BP range, (ΔTBP > 13 °C). The different effects on the BP may be due to the AuNPs accumulating at singular defect sites whereas the mini-AuNRs, with diameters smaller than that of the disclination lines, can more efficiently fill in the BP defects.

Remote control of charge transport and chiral induction along a DNA-metallohelicate.

Herein we present a new strategy to achieve chiral induction and redox switching along the backbone of metallohelicate architectures, wherein a DNA duplex directs the handedness and charge transport properties of a metal-organic assembly more than 60 bonds away (a distance of >10 nm). The quantitative and site-specific binding of copper(i) ions to DNA-templated coordination sites imparts enhanced thermodynamic stability to the assembly, while the DNA duplex transfers its natural right-handed helicity to the proximal and distal metal centers of the helicates. When copper(ii) ions are employed instead of copper(i) ions, spontaneous DNA-mediated reduction occurs, which we propose is followed by a slower change in coordination environment (from pentacoordinate CuII to tetrahedral CuI) to generate copper(i) helicates. We demonstrate that the reduction of the adjacent and distal bis-phenanthroline sites is dependent on their proximity to DNA guanine bases (which act as the electron source). The kinetics of helical charge transport can thus be tuned based on guanine-CuII separation, resulting in a sequence- and distance-dependent redox switch that transfers electronic information from DNA to multiple linearly-arranged metal centers.

Polymer functionalized nanoparticles in liquid crystals: combining PDLCs with LC nanocomposites.

Liquid crystal (LC)-polymer blends are important stimuli responsive materials already employed in a wide range of applications whereas nanoparticle (NP)-LC blends are an emerging class of nanocomposites. Polymer ligands offer the advantages of synthetic simplicity along with chemical and molecular weight tunability. Here we compare the phase behavior of 5CB blended with poly(ethylene oxide) (PEO) and with gold NPs functionalized with thiolated PEO (AuNP-PEO) as a function of PEO concentration by DSC, POM and 13C NMR spectroscopy. Both PEO and the AuNP-PEO form uniform dispersions in isotropic 5CB and phase separate below the I-N phase transition temperature. Above the PEO crystallization temperature, the PEO/5CB blends show the expected biphasic state of PEO rich-isotropic liquid co-existing with PEO-poor nematic droplets. At PEO concentrations above 10 wt%, nematic 5CB nucleates with PEO crystallization. Both PEO and AuNP-PEO induce homeotropic alignment of the 5CB matrix immediately below TNI. The AuNP-PEO/5CB blends form thermally reversible cellular networks similar to AuNPs functionalized with low molecular weight mesogenic ligands. A thermodynamic model to account for the observed phase behavior is presented.

Micromechanical Redox Actuation by Self-Assembled Monolayers of Ferrocenylalkanethiolates: Evens Push More Than Odds.

Microcantilever transducers can be valuable tools for the investigation of physicochemical processes in organized molecular films. Gold-coated cantilevers are used here to investigate the electrochemomechanics of redox-active self-assembled monolayers (SAMs) of ferrocenylalkanethiolates (Fc(CH2) nS) of different alkyl chain lengths. A significant odd-even effect is observed in the surface stress and cantilever movement generated by the oxidation of the SAM-confined ferrocenes as the number of methylene units n in the SAM backbone is varied. We demonstrate that stronger alkyl chain-chain interactions are at the origin of the larger surface stresses generated by SAMs with an even versus odd n. The findings highlight the impact of subtle structural effects and weak van der Waals interactions on the mechanical actuation produced by redox reactions in self-assembled systems.

DNA-imprinted polymer nanoparticles with monodispersity and prescribed DNA-strand patterns.

As colloidal self-assembly increasingly approaches the complexity of natural systems, an ongoing challenge is to generate non-centrosymmetric structures. For example, patchy, Janus or living crystallization particles have significantly advanced the area of polymer assembly. It has remained difficult, however, to devise polymer particles that associate in a directional manner, with controlled valency and recognition motifs. Here, we present a method to transfer DNA patterns from a DNA cage to a polymeric nanoparticle encapsulated inside the cage in three dimensions. The resulting DNA-imprinted particles (DIPs), which are 'moulded' on the inside of the DNA cage, consist of a monodisperse crosslinked polymer core with a predetermined pattern of different DNA strands covalently 'printed' on their exterior, and further assemble with programmability and directionality. The number, orientation and sequence of DNA strands grafted onto the polymeric core can be controlled during the process, and the strands are addressable independently of each other.

Selective in situ potential-assisted SAM formation on multi electrode arrays.

The selective modification of individual components in a biosensor array is challenging. To address this challenge, we present a generalizable approach to selectively modify and characterize individual gold surfaces in an array, in an in situ manner. This is achieved by taking advantage of the potential dependent adsorption/desorption of surface-modified organic molecules. Control of the applied potential of the individual sensors in an array where each acts as a working electrode provides differential derivatization of the sensor surfaces. To demonstrate this concept, two different self-assembled monolayer (SAM)-forming electrochemically addressable ω-ferrocenyl alkanethiols (C11) are chemisorbed onto independent but spatially adjacent gold electrodes. The ferrocene alkanethiol does not chemisorb onto the surface when the applied potential is cathodic relative to the adsorption potential and the electrode remains underivatized. However, applying potentials that are modestly positive relative to the adsorption potential leads to extensive coverage within 10 min. The resulting SAM remains in a stable state while held at potentials <200 mV above the adsorption potential. In this state, the chemisorbed SAM does not significantly desorb nor do new ferrocenylalkythiols adsorb. Using three set applied potentials provides for controlled submonolayer alkylthiol marker coverage of each independent gold electrode. These three applied potentials are dependent upon the specifics of the respective adsorbate. Characterization of the ferrocene-modified electrodes via cyclic voltammetry demonstrates that each specific ferrocene marker is exclusively adsorbed to the desired target electrode.

Hydrogen-Bonded Liquid Crystal Nanocomposites.

Nanoparticle-liquid crystal (NP-LC) composites based on hydrogen bonding were explored using a model system. The ligand shells of 3 nm diameter zirconium dioxide nanoparticles (ZrO2 NPs) were varied to control their interaction with 4-n-hexylbenzoic acid (6BA). The miscibility and effect of the NPs on the nematic order as a function of particle concentration was characterized by polarized optical microscopy (POM), fluorescence microscopy and (2)H NMR spectroscopy. Nonfunctionalized ZrO2 NPs have the lowest miscibility and strongest effect on the LC matrix due to irreversible binding of 6BA to the NPs via a strong zirconium carboxylate bond. The ZrO2 NPs were functionalized with 6-phosphonohexanoic acid (6PHA) or 4-(6-phosphonohexyloxy)benzoic acid (6BPHA) which selectively bind to the ZrO2 NP surface via the phosphonic acid groups. The miscibility was increased by controlling the concentration of the pendant CO2H groups by adding hexylphosphonic acid (HPA) to act as a spacer group. Fluorescence microscopy of lanthanide doped ZrO2 NPs showed no aggregates in the nematic phase below the NP concentration where aggregates are observed in the isotropic phase. The functionalized NPs preferably concentrate into LC defects and any remaining isotropic liquid but are still present throughout the nematic liquid at a lower concentration.

Reprogramming the assembly of unmodified DNA with a small molecule.

The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA 'alphabet' by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces, reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid (PNA) all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials.

Reversible Nanoparticle Cubic Lattices in Blue Phase Liquid Crystals.

Blue phases (BPs), a distinct class of liquid crystals (LCs) with 3D periodic ordering of double twist cylinders involving orthogonal helical director twists, have been theoretically studied as potential templates for tunable colloidal crystals. Here, we report the spontaneous formation of thermally reversible, cubic crystal nanoparticle (NP) assemblies in BPs. Gold NPs, functionalized to be highly miscible in cyanobiphenyl-based LCs, were dispersed in BP mixtures and characterized by polarized optical microscopy and synchrotron small-angle X-ray scattering (SAXS). The NPs assemble by selectively migrating to periodic strong trapping sites in the BP disclination lines. The NP lattice, remarkably robust given the small particle size (4.5 nm diameter), is commensurate with that of the BP matrix. At the BP I to BP II phase transition, the NP lattice reversibly switches between two different cubic structures. The simultaneous presence of two different symmetries in a single material presents an interesting opportunity to develop novel dynamic optical materials.

Modulation of charge transport across double-stranded DNA by the site-specific incorporation of copper bis-phenanthroline complexes.

The site-specific incorporation of transition-metal complexes within DNA duplexes, followed by their immobilization on a gold surface, was studied by electrochemistry to characterize their ability to mediate charge. Cyclic voltammetry, square-wave voltammetry, and control experiments were carried out on fully matched and mismatched DNA strands that are mono- or bis-labeled with transition-metal complexes. These experiments are all consistent with the ability of the metal centers to act as a redox probe that is well coupled to the DNA π-stack, allowing DNA-mediated charge transport.

Switching the Z/E selectivity in the palladium(II)-catalyzed decarboxylative Heck arylations of trans-cinnamaldehydes by solvent.

The Z/E selectivity of Pd(II)-catalyzed decarboxylative Heck-type arylations of trans-cinnamaldehydes can be controlled readily by switching the reaction solvent. Depending on the type of solvent used, each of the two isomeric products can be obtained with good to excellent Z/E ratio. In THF, Z-isomers were formed preferentially, whereas DMF provided the E-isomers predominantly.

Microcantilevers bend to the pressure of clustered redox centers.

The redox-activated deflection of microcantilevers has attracted interest for nanoactuation and chemical sensing. Microcantilever sensors are devices that transduce (bio)chemical reactions into a quantifiable nanomechanical motion via surface stress changes. Despite promising applications in analytical science, poor signal-to-noise ratios and a limited understanding of the molecular origins of the surface stress changes that cause the observed deflections remain obstacles to cantilever-based sensing becoming an established (bio)detection method, such as surface plasmon resonance and electrochemistry. We use phase-separated, binary self-assembled monolayers (SAMs) of ferrocenyldodecanethiolate and n-undecanethiolate as a model system to study the effect of the steric crowding of the redox centers on the surface stress change and cantilever deflection produced by the electrochemical oxidation of the surface-tethered ferrocene to ferrocenium. We correlate the measured surface stress change to the fraction of the clustered ferrocenyldodecanethiolate phase in the binary SAMs. The pairing of anions with the sterically crowded clustered ferroceniums induces a collective molecular reorientation which drives the cantilever deflection. The results provide fundamental insights into the response mechanism of microcantilever-based actuating and sensing technologies.

Redox-induced ion pairing of anionic surfactants with ferrocene-terminated self-assembled monolayers: Faradaic electrochemistry and surfactant aggregation at the monolayer/liquid interface.

Oxidoreduction of self-assembled monolayers (SAMs) of ferrocenyldodecanethiolate on gold in aqueous solutions of surface-active sodium n-alkyl sulfates (NaCnSO4) of 6, 8, 10, and 12 carbons is investigated by cyclic voltammetry and surface plasmon resonance. The effects of surfactant micellization and alkyl chain length on the redox response of the surface-tethered ferrocenes are examined. The SAM redox electrochemistry is sensitive to the surfactant aggregation state in solution. The nonideal behavior of the sodium alkyl sulfates at concentrations above the critical micelle concentration leads to a non-Nernstian variation of the SAM redox potential with concentration. The presence of micelles in solution results in decreased anodic-to-cathodic peak separations and anodic peak full widths at half-maximum. A longer alkyl chain length results in an increased ability of the alkyl sulfate anion to ion pair with the SAM-bound ferrocenium, resulting in oxidation of the ferrocene at lower potential. A comparison of the SAM redox potential at a fixed surfactant concentration of ideal behavior suggests a 4.5 × 10(4) difference in the ion-pairing abilities of the shorter-chain C6SO4(-) and longer-chain C12SO4(-). One-half of the available SAM-bound ferrocenes are oxidized in the NaCnSO4 electrolyte. Surfactant anions adsorb and assemble onto the SAM surface by specific ion-pairing interactions between the sulfate headgroups and oxidized ferrocenium species, forming an interdigitated monolayer in which the surfactant anions alternate between a heads-down and heads-up orientation with respect to the SAM. The work presented points to applications of ferrocenylalkanethiolate SAMs as anion-selective membranes, probes of micelle formation, and surfaces for the electrochemically switchable assembly of organosulfates.

A molecular and thermodynamic view of the assembly of gold nanoparticles in nematic liquid crystal.

The molecular interactions driving the assembly of gold nanoparticles (AuNPs) in a nematic liquid crystal (LC) are directly detected by nuclear magnetic resonance (NMR) spectroscopy and thermodynamically analyzed. The orientational orders of the selectively deuterated LC matrix and AuNP ligands, each separately followed by variable temperature (2)H NMR as a function of particle concentration, were observed to be strongly correlated. The mechanism of the reversible formation of long-range, quasi-periodic nanoparticle structures is attributed to the coupling of the AuNP ligands to the LC matrix, inducing an isotropic-nematic biphasic state. Experimentally validated thermodynamic modeling shows that, in contrast to colloidal nematics that are dominated by elastic forces, nematic dispersions of nanoparticles self-organize through a subtle balance of entropic forces and excluded volume, interface-mediated mesogen and nanoparticle molecular interactions, and couplings between conserved and nonconserved order parameters. Fine-tuning of these interactions through ligand and mesogen chemistry, together with mesoscale modeling, provides a route for materials innovations by merging structured fluid physics and nanoscience.

The role of organic linkers in directing DNA self-assembly and significantly stabilizing DNA duplexes.

We show a simple method to control both the stability and the self-assembly behavior of DNA structures. By connecting two adjacent duplexes with small synthetic linkers, factors such as linker rigidity and DNA strand orientation can increase the thermal denaturation temperature of 17 base-pair duplexes by up to 10 °C, and significantly increase the cooperativity of melting of the two duplexes. The same DNA sequence can thus be tuned to melt at vastly different temperatures by selecting the linker structure and DNA-to-linker connectivity. In addition, a small rigid m-triphenylene linker directly affects the self-assembly product distribution. With this linker, changes in the orientation of the linked strands (e.g., 5'3' vs 3'3') can lead to dramatic changes in the self-assembly behavior, from the formation of cyclic dimer and tetramer to higher-order oligomers. These variations can be readily predicted using a simple strand-end alignment model.