Reversible strain-promoted DNA polymerization.

Molecular strain can be introduced to influence the outcome of chemical reactions. Once a thermodynamic product is formed, however, reversing the course of a strain-promoted reaction is challenging. Here, a reversible, strain-promoted polymerization in cyclic DNA is reported. The use of nonhybridizing, single-stranded spacers as short as a single nucleotide in length can promote DNA cyclization. Molecular strain is generated by duplexing the spacers, leading to ring opening and subsequent polymerization. Then, removal of the strain-generating duplexers triggers depolymerization and cyclic dimer recovery via enthalpy-driven cyclization and entropy-mediated ring contraction. This reversibility is retained even when a protein is conjugated to the DNA strands, and the architecture of the protein assemblies can be modulated between bivalent and polyvalent states. This work underscores the utility of using DNA not only as a programmable ligand for assembly but also as a route to access restorable bonds, thus providing a molecular basis for DNA-based materials with shape-memory, self-healing, and stimuli-responsive properties.

Space-tiled colloidal crystals from DNA-forced shape-complementary polyhedra pairing.

Generating space-filling arrangements of most discrete polyhedra nanostructures of the same shape is not possible. However, if the appropriate individual building blocks are selected (e.g., cubes), or multiple shapes of the appropriate dimensions are matched (e.g., octahedra and tetrahedra) and their pairing interactions are subsequently forced, space-filled architectures may be possible. With flexible molecular ligands (polyethylene glycol-modified DNA), the shape of a polyhedral nanoparticle can be deliberately altered and used to realize geometries that favor space tessellation. In this work, 10 new colloidal crystals were synthesized from DNA-modified nanocrystal building blocks that differed in shapes and sizes, designed to form space-filling architectures with micron-scale dimensions. The insights and capabilities provided by this new strategy substantially expand the scope of colloidal crystals possible and provide an expanded tool kit for researchers interested in designing metamaterials.

Amphiphilic dendrons as supramolecular holdase chaperones.

The aggregation of incompletely or incorrectly folded proteins is implicated in diseases including Alzheimer's, cataracts, and other maladies. Natural systems express protein chaperones to prevent or even reverse harmful protein aggregation. Synthetic chaperone-like systems have sought to mimic the action of their biological counterparts but typically require substantial optimization and high concentrations to be functional, or lack programmability that would enable the targeting of specific protein substrates. Here we report a series of amphiphilic dendrons that undergo assembly and inhibit the aggregation of fragment 16-22 amyloid ß protein (Aß16-22). We show that monodisperse dendrons with hydrophilic tetraethylene glycol chains and a hydrophobic core based on naphthyl and benzyl ethers undergo supramolecular assembly in aqueous solutions to form sphere-like particles. The solubility of these dendrons and their assemblies is tuned by varying the relative sizes of their hydrophilic and hydrophobic regions. Two water-soluble dendrons are discovered and shown, via fluorescence experiments with rhodamine 6G, to generate a hydrophobic environment. Furthermore, we demonstrate that sub-stoichiometric concentrations of these amphiphilic dendrons stabilize Aß16-22 peptide with respect to aggregation, mimicking the activity of holdase chaperones. Our results highlight the potential of these amphiphilic molecules as the basis for a novel approach to artificial chaperones that may address many of the challenges associated with existing synthetic chaperone mimics.

Open-channel metal particle superlattices.

Although tremendous advances have been made in preparing porous crystals from molecular precursors1,2, there are no general ways of designing and making topologically diversified porous colloidal crystals over the 10-1,000 nm length scale. Control over porosity in this size range would enable the tailoring of molecular absorption and storage, separation, chemical sensing, catalytic and optical properties of such materials. Here, a universal approach for synthesizing metallic open-channel superlattices with pores of 10 to 1,000 nm from DNA-modified hollow colloidal nanoparticles (NPs) is reported. By tuning hollow NP geometry and DNA design, one can adjust crystal pore geometry (pore size and shape) and channel topology (the way in which pores are interconnected). The assembly of hollow NPs is driven by edge-to-edge rather than face-to-face DNA-DNA interactions. Two new design rules describing this assembly regime emerge from these studies and are then used to synthesize 12 open-channel superlattices with control over crystal symmetry, channel geometry and topology. The open channels can be selectively occupied by guests of the appropriate size and that are modified with complementary DNA (for example, Au NPs).

The emergence of valency in colloidal crystals through electron equivalents.

Colloidal crystal engineering of complex, low-symmetry architectures is challenging when isotropic building blocks are assembled. Here we describe an approach to generating such structures based upon programmable atom equivalents (nanoparticles functionalized with many DNA strands) and mobile electron equivalents (small particles functionalized with a low number of DNA strands complementary to the programmable atom equivalents). Under appropriate conditions, the spatial distribution of the electron equivalents breaks the symmetry of isotropic programmable atom equivalents, akin to the anisotropic distribution of valence electrons or coordination sites around a metal atom, leading to a set of well-defined coordination geometries and access to three new low-symmetry crystalline phases. All three phases represent the first examples of colloidal crystals, with two of them having elemental analogues (body-centred tetragonal and high-pressure gallium), while the third (triple double-gyroid structure) has no known natural equivalent. This approach enables the creation of complex, low-symmetry colloidal crystals that might find use in various technologies.

An Accelerated Modular-Orthogonal Ni-Catalyzed Methodology to Symmetric and Nonsymmetric Constitutional Isomeric AB2 to AB9 Dendrons Exhibiting Unprecedented Self-Organizing Principles.

Five libraries of natural and synthetic phenolic acids containing five AB3, ten constitutional isomeric AB2, one AB4, and one AB5 were previously synthesized and reported by our laboratory in 5 to 11 steps. They were employed to construct seven libraries of self-assembling dendrons, by divergent generational, deconstruction, and combined approaches, enabling the discovery of a diversity of supramolecular assemblies including Frank-Kasper phases, soft quasicrystals, and complex helical organizations, some undergoing deracemization in the crystal state. However, higher substitution patterns within a single dendron were not accessible. Here we report three libraries consisting of 30 symmetric and nonsymmetric constitutional isomeric phenolic acids with unprecedented sequenced patterns, including two AB2, three AB3, eight AB4, five AB5, six AB6, three AB7, two AB8, and one AB9 synthesized by accelerated modular-orthogonal Ni-catalyzed borylation and cross-coupling. A single etherification step with 4-(n-dodecyloxy)benzyl chloride transformed all these phenolic acids, of interest also for other applications, into self-assembling dendrons. Despite this synthetic simplicity, they led to a diversity of unprecedented self-organizing principles: lamellar structures of interest for biological membrane mimics, helical columnar assemblies from rigid-solid angle dendrons forming Tobacco Mosaic Virus-like assemblies, columnar organizations from adaptable-solid angle dendrons forming disordered micellar-like nonhelical columns, columns from supramolecular spheres, five body-centered cubic phases displaying supramolecular orientational memory, rarely encountered in previous libraries forming predominantly Frank-Kasper phases, and two Frank-Kasper phases. Lessons from these self-organizing principles, discovered within a single generation of self-assembling dendrons, may help elaborate design principles for complex helical and nonhelical organizations of synthetic and biological matter.

Encoding hierarchical assembly pathways of proteins with DNA.

The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multistep, hierarchical assembly pathways. Achieving similar complexity in synthetic materials through hierarchical assembly is challenging due to difficulties with defining multiple recognition areas on synthetic building blocks and controlling the sequence through which those recognition sites direct assembly. Here, we show that we can exploit the chemical anisotropy of proteins and the programmability of DNA ligands to deliberately control the hierarchical assembly of protein-DNA materials. Through DNA sequence design, we introduce orthogonal DNA interactions with disparate interaction strengths ("strong" and "weak") onto specific geometric regions of a model protein, stable protein 1 (Sp1). We show that the spatial encoding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first stage of assembly increases the multivalency of weak DNA-DNA interactions that give rise to an emergent second stage of assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway but can also direct distinct structural outcomes from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the structural and chemical information necessary into building blocks to program their multistep hierarchical assembly. Our findings represent a strategy for controlling the hierarchical assembly of proteins to realize a diverse set of protein-DNA materials by design.

Redefining Protein Interfaces within Protein Single Crystals with DNA.

Proteins are exquisite nanoscale building blocks: molecularly pure, chemically addressable, and inherently selective for their evolved function. The organization of proteins into single crystals with high positional, orientational, and translational order results in materials where the location of every atom can be known. However, controlling the organization of proteins is challenging due to the myriad interactions that define protein interfaces within native single crystals. Recently, we discovered that introducing a single DNA-DNA interaction between protein surfaces leads to changes in the packing of proteins within single crystals and the protein-protein interactions (PPIs) that arise. However, modifying specific PPIs to effect deliberate changes to protein packing is an unmet challenge. In this work, we hypothesized that disrupting and replacing a highly conserved PPI with a DNA-DNA interaction would enable protein packing to be modulated by exploiting the programmability of the introduced oligonucleotides. Using concanavalin A (ConA) as a model protein, we circumvent potentially deleterious mutagenesis and exploit the selective binding of ConA toward mannose to noncovalently attach DNA to the protein surface. We show that DNA association eliminates the major PPI responsible for crystallization of native ConA, thereby allowing subtle changes to DNA design (length, complementarity, and attachment position) to program distinct changes to ConA packing, including the realization of three novel crystal structures and the deliberate expansion of ConA packing along a single crystallographic axis. These findings significantly enhance our understanding of how DNA can supersede native PPIs to program protein packing within ordered materials.

Programming Fluorogenic DNA Probes for Rapid Detection of Steroids.

The ability of aptamers to recognize a variety of different molecules has fueled their emergence as recognition agents to probe complex media and cells. Many detection strategies require aptamer binding to its target to result in a dramatic change in structure, typically from an unfolded to a folded state. Here, we report a strategy based on forced intercalation (FIT) that increases the scope of aptamer recognition by transducing subtle changes in aptamer structures into fluorescent readouts. By screening a library of green-fluorescent FIT-aptamers whose design is guided by computational modeling, we could identify hits that sense steroids like dehydroepiandrosterone sulfate (DHEAS) down to 1.3 µM with no loss in binding affinity compared to the unmodified aptamer. This enabled us to study DHEAS in clinical serum samples with several advantages over gold standard methods, including rapid readout (<30 min), simple instrumentation (plate-reader), and low sample volumes (10 µL).

Enhanced Concanavalin†A Binding to Preorganized Mannose Nanoarrays in Glycodendrimersomes Revealed Multivalent Interactions.

The effect of the two-dimensional glycan display on glycan-lectin recognition remains poorly understood despite the importance of these interactions in a plethora of cellular processes, in (patho)physiology, as well as its potential for advanced therapeutics. Faced with this challenge we utilized glycodendrimersomes, a type of synthetic vesicles whose membrane mimics the surface of a cell and offers a means to probe the carbohydrate biological activity. These single-component vesicles were formed by the self-assembly of sequence-defined mannose-Janus dendrimers, which serve as surrogates for glycolipids. Using atomic force microscopy and molecular modeling we demonstrated that even mannose, a monosaccharide, was capable of organizing the sugar moieties into periodic nanoarrays without the need of the formation of liquid-ordered phases as assumed necessary for rafts. Kinetics studies of Concanavalin A binding revealed that those nanoarrays resulted in a new effective ligand yielding a ten-fold increase in the kinetic and thermodynamic constant of association.

Monodisperse Macromolecules by Self-Interrupted Living Polymerization.

Biological macromolecules such as proteins and nucleic acids are monodisperse just as low-molar-mass organic compounds are. However, synthetic macromolecules contain mixtures of different chain lengths, the most uniform being generated by living polymerizations, which exhibit a maximum of 1-3% of chains with the desired length. Monodisperse natural and synthetic oligomers can be obtained in low quantities by tedious, multistep iterative methods. Here we report a methodology to synthesize monodisperse synthetic macromolecules by self-interrupted living polymerization. This methodology relies on a concept that combines supramolecular and macromolecular chemistry and differs from the conventional reactivity principles employed in the synthesis of polymers for over 100 years.

Extraordinary Acceleration of Cogwheel Helical Self-Organization of Dendronized Perylene Bisimides by the Dendron Sequence Encoding Their Tertiary Structure.

The cogwheel model of hierarchical self-organization provides a route to highly ordered crystalline helical columnar hexagonal arrays of perylene bisimides (PBIs) conjugated to (3,4,5)-dimethyloctyl (racemic dm8*, r) minidendrons. Cogwheel PBIs assemble with identical structural order irrespective of molecular chirality to generate helical columns jacketed with an alkyl coat with length equal to half the helical pitch, exhibiting helical deracemization in the crystal state. These assemblies were accessible only via annealing or cooling and reheating at 1 °C/min. Recently it was discovered that hybrid rr8 sequence-defined dendrons with r and linear n-octyl (8) chains enabled the formation of the cogwheel phase at 10 °C/min upon heating but not cooling. Here we report four libraries of hybrid PBIs with sequence-defined dendrons containing r and n-alkyl (CnH2n+1) chains with n = 6, 7, 9, and 10. Structural analysis of these libraries by fiber X-ray diffraction and differential scanning calorimetry reveals that the 9r9 sequence enables an extraordinary acceleration of cogwheel assembly at rates of up to 50 °C/min on heating and cooling, providing, to the best of our knowledge, the fastest crystallizing supramolecular or covalent macromolecule known. Solid-state NMR studies help to elucidate this unexpected and unprecedented extraordinary acceleration of hierarchical self-organization, which arises from a combination of crystal packing of the ideal tertiary structure and alkyl chain dynamics. This general model raises questions about the use of achiral motifs to achieve high structural order in chiral systems and the need for disorder to create order in complex biological and bioinspired synthetic systems.

DNA- and Field-Mediated Assembly of Magnetic Nanoparticles into High-Aspect Ratio Crystals.

Under an applied magnetic field, superparamagnetic Fe3 O4 nanoparticles with complementary DNA strands assemble into crystalline, pseudo-1D elongated superlattice structures. The assembly process is driven through a combination of DNA hybridization and particle dipolar coupling, a property dependent on particle composition, size, and interparticle distance. The DNA controls interparticle distance and crystal symmetry, while the magnetic field leads to anisotropic crystal growth. Increasing the dipole interaction between particles by increasing particle size or external field strength leads to a preference for a particular crystal morphology (e.g., rhombic dodecahedra, stacked clusters, and smooth rods). Molecular dynamics simulations show that an understanding of both DNA hybridization energetic and magnetic interactions is required to predict the resulting crystal morphology. Taken together, the data show that applied magnetic fields with magnetic nanoparticles can be deliberately used to access nanostructures beyond what is possible with DNA hybridization alone.

Sequence-Defined Dendrons Dictate Supramolecular Cogwheel Assembly of Dendronized Perylene Bisimides.

A dendronized perylene bisimide (PBI) that self-organizes into hexagonal arrays of supramolecular double helices with identical single-crystal-like order that disregards chirality was recently reported. A cogwheel model of self-assembly that explains this process was proposed. Accessing the highly ordered cogwheel phase required very slow heating and cooling or extended periods of annealing. Analogous PBIs with linear alkyl chains did not exhibit the cogwheel assembly. Here a library of sequence-defined dendrons containing all possible compositions of linear and racemic alkyl chains was employed to construct self-assembling PBIs. Thermal and structural analysis of their assemblies by differential scanning calorimetry (DSC) and fiber X-ray diffraction (XRD) revealed that the incorporation of n-alkyl chains accelerates the formation of the high order cogwheel phase, rendering the previously invisible phase accessible under standard heating and cooling rates. Small changes to the primary structure, as constitutional isomerism, result in significant changes to macroscopic properties such as melting of the periodic array. This study demonstrated how changes to the sequence-defined primary structure, including the relocation of methyl groups between two constitutional isomers, dictate tertiary and quaternary structure in hierarchical assemblies. This led to the discovery of a sequence that self-organizes the cogwheel assembly much faster than even the corresponding homochiral compounds and demonstrated that defined-sequence, which has long been recognized as a determinant for the complex structure of biomacromolecules including proteins and nucleic acids, plays the same role also in supramolecular synthetic systems.

Supramolecular Spheres Self-Assembled from Conical Dendrons Are Chiral.

Frank-Kasper phases and liquid quasicrystals self-organize from supramolecular spheres of dendrimers, block copolymers, surfactants and other self-assembling molecules. These spheres are expected to be achiral due to their isotropic shape. Nevertheless, supramolecular spheres from short helical stacks of crown-like dendrimers self-organize a Pm3̅ n cubic (Frank-Kasper A15) phase which exhibits chirality on the macroscopic scale. However, the chirality of classic isotropic supramolecular micellar-like spheres, generated from conical dendrons, is unknown. Here we report a library of second and third generation biphenylpropyl dendrons with chiral groups at their apex that produces single-handed chiral supramolecular spheres. Up to 480 conical dendrons self-assemble to form micellar-like spheres, with a molar mass of up to 1.1 × 106 g/mol, that self-organize into a Pm3̅ n phase with chirality detectable on the macroscopic scale. This demonstration of chirality in micellar-like spheres of a Frank-Kasper phase raises the fundamental question whether micellar-like spheres forming 3D phases generated from other soft matter such as block copolymers, surfactants, and other molecules are chiral.

Encoding biological recognition in a bicomponent cell-membrane mimic.

Self-assembling dendrimers have facilitated the discovery of periodic and quasiperiodic arrays of supramolecular architectures and the diverse functions derived from them. Examples are liquid quasicrystals and their approximants plus helical columns and spheres, including some that disregard chirality. The same periodic and quasiperiodic arrays were subsequently found in block copolymers, surfactants, lipids, glycolipids, and other complex molecules. Here we report the discovery of lamellar and hexagonal periodic arrays on the surface of vesicles generated from sequence-defined bicomponent monodisperse oligomers containing lipid and glycolipid mimics. These vesicles, known as glycodendrimersomes, act as cell-membrane mimics with hierarchical morphologies resembling bicomponent rafts. These nanosegregated morphologies diminish sugar-sugar interactions enabling stronger binding to sugar-binding proteins than densely packed arrangements of sugars. Importantly, this provides a mechanism to encode the reactivity of sugars via their interaction with sugar-binding proteins. The observed sugar phase-separated hierarchical arrays with lamellar and hexagonal morphologies that encode biological recognition are among the most complex architectures yet discovered in soft matter. The enhanced reactivity of the sugar displays likely has applications in material science and nanomedicine, with potential to evolve into related technologies.

Dendronized Poly(2-oxazoline) Displays within only Five Monomer Repeat Units Liquid Quasicrystal, A15 and σ Frank-Kasper Phases.

Liquid quasicrystals (LQC) have been discovered in self-assembling benzyl ether, biphenylmethyl ether, phenylpropyl ether, biphenylpropyl ether and some of their hybrid dendrons and subsequently in block copolymers, surfactants and other assemblies. These quasiperiodic arrays, which lack long-range translational periodicity, are approximated by two Frank-Kasper periodic arrays, Pm3̅ n cubic (Frank-Kasper A15) and P42/ mnm tetragonal (Frank-Kasper σ), which have been discovered in complex soft matter in the same order and compounds. Poly(2-oxazoline)s dendronized with (3,4) nG1 minidendrons (where n denotes an alkyl chain, C nH2 n+1) self-organize into the Pm3̅ n cubic phase ( n = 14 and 15) and, as reported recently, the P42/ mnm tetragonal phase ( n = 16). However, no LQC of a poly(2-oxazoline) is yet known. Here we report the synthesis, structural and retrostructural analysis of a dendronized poly(2-oxazoline) with n = 17 which self-organizes not only into the LQC but also in the above two Frank-Kasper approximants. All three phases are observed from the same polymer within a very narrow range of degree of polymerization that corresponds to only five monomer repeat units (5 ≤ DP ≤ 10). The formation of the Pm3̅ n cubic, P42/ mnm tetragonal and LQC phases from a single polymer chain within such a narrow range of DP raises the questions of how and why each of these phases is self-organized. This system may provide a model for theoretical investigations into the self-organization of soft matter into Frank-Kasper and related periodic and quasiperiodic arrays.

Hierarchical Self-Organization of Chiral Columns from Chiral Supramolecular Spheres.

The supramolecular column is an archetypal architecture in the field of periodic liquid crystalline and crystalline arrays. Columns are generated via self-assembly, coassembly, and polymerization of monomers containing molecules shaped as discs, tapered, twin- and Janus-tapered, crowns, hat-shaped crowns, and fragments thereof. These supramolecular columns can be helical and therefore exhibit chirality. In contrast, spheres represent a fundamentally distinct architecture, generated from conical and crown-like molecules, which self-organize into body-centered cubic, Pm3̅ n cubic (also known as Frank-Kasper A15), and tetragonal (also known as Frank-Kasper σ) phases. Supramolecular spherical aggregates are not known to further assemble into a columnar architecture, except as an intermediate state between a columnar periodic array and a cubic phase. In the present work, a chiral dendronized cyclotetraveratrylene (CTTV) derivative is demonstrated to self-organize into a supramolecular column unexpectedly constructed from supramolecular spheres, with no subsequent transition to a cubic phase. Structural and retrostructural analysis using a combination of differential scanning calorimetry, X-ray diffraction (XRD), molecular modeling, and simulation of XRD patterns reveals that this CTTV derivative, which is functionalized with eight chiral first-generation minidendrons, self-organizes via a column-from-spheres model. The transition from column to column-from-spheres was monitored by circular dichroism spectroscopy, which demonstrated that both the supramolecular column and supramolecular spheres are chiral. This column-from-spheres model, which unites two fundamentally distinct self-assembled architectures, provides a new mechanism to self-organize supramolecular columnar architectures.

Tetrahedral Arrangements of Perylene Bisimide Columns via Supramolecular Orientational Memory.

Chiral, shape, and liquid crystalline memory effects are well-known to produce commercial macroscopic materials with important applications as springs, sensors, displays, and memory devices. A supramolecular orientational memory effect that provides complex nanoscale arrangements was only recently reported. This supramolecular orientational memory was demonstrated to preserve the molecular orientation and packing within supramolecular units of a self-assembling cyclotriveratrylene crown at the nanoscale upon transition between its columnar hexagonal and Pm3̅n cubic periodic arrays. Here we report the discovery of supramolecular orientational memory in a dendronized perylene bisimide (G2-PBI) that self-assembles into tetrameric crowns and subsequently self-organizes into supramolecular columns and spheres. This supramolecular orientation memory upon transition between columnar hexagonal and body-centered cubic (BCC) mesophases preserves the 3-fold cubic [111] orientations rather than the 4-fold [100] axes, generating an unusual tetrahedral arrangement of supramolecular columns. These results indicate that the supramolecular orientational memory concept may be general for periodic arrays of self-assembling dendrons and dendrimers as well as for other periodic and quasiperiodic nanoscale organizations comprising supramolecular spheres, generated from other organized complex soft matter including block copolymers and surfactants.

Complex Arrangement of Orthogonal Nanoscale Columns via a Supramolecular Orientational Memory Effect.

Memory effects, including shape, chirality, and liquid-crystallinity, have enabled macroscopic materials with novel functions. However, the generation of complex supramolecular nanosystems via memory effects has not yet been investigated. Here, we report a cyclotriveratrylene-crown (CTV) compound that self-assembles into supramolecular columns and spheres forming, respectively, hexagonal and cubic mesophases. Upon transition from one phase to the other, an epitaxial relationship holds, via an unprecedented supramolecular orientational memory effect. Specifically, the molecular orientation and columnar character of supramolecular packing is preserved in the cubic phase, providing an otherwise inaccessible structure comprising orthogonally oriented domains of supramolecular columns. The continuous columnar character of tetrahedrally distorted supramolecular spheres self-organized from the CTV derivative in the faces of the Pm3̅n lattice is the basis of this supramolecular orientational memory, which holds throughout cycling in temperature between the two phases. This concept is expected to be general for other combinations of periodic and quasiperiodic arrays generated from supramolecular spheres upon transition to supramolecular columns.