Collective helicity switching of a DNA-coat assembly

Mechanistic Insights into the Self-Assembly of an Acid-Sensitive Photoresponsive Supramolecular Polymer

The supramolecular polymerization of an acid‐sensitive pyridyl‐based ligand (L₁) bearing a photoresponsive azobenzene moiety was elucidated by mechanistic studies. Addition of trifluoroacetic acid (TFA) led to the transformation of the antiparallel H‐bonded fibers of L₁ in methylcyclohexane into superhelical braid‐like fibers stabilized by H‐bonding of parallel‐stacked monomer units. Interestingly, L₁ dimers held together by unconventional pyridine–TFA N⋅⋅⋅H⋅⋅⋅O bridges represent the main structural elements of the assembly. UV‐light irradiation caused a strain‐driven disassembly and subsequent aggregate reconstruction, which ultimately led to short fibers. The results allowed to understand the mechanism of mutual influence of acid and light stimuli on supramolecular polymerization processes, thus opening up new possibilities to design advanced stimuli‐triggered supramolecular systems.

Praseodymium promotes B–Z transition in self-assembled DNA nanostructures

Millimolar concentrations of PrCl₃ can induce sequence-specific B–Z transition in various-self-assembled branched DNA (bDNA) nanostructures. Competitive dye binding and thermal kinetics suggest that the phosphate backbone and grooves of bDNA are wrapped with Pr³⁺ for stabilizing the Z-bDNA. Application of EDTA can convert Z-DNA back to the B-form.

Millimolar concentrations of PrCl₃ can induce sequence-specific B–Z transition in various-self-assembled branched DNA (bDNA) nanostructures.

Chiral nanostructures self-assembled from nitrocinnamic amide amphiphiles: substituent and solvent effects

Chiral nanostructures, such as α-helical proteins and double helix DNA, are widely found in biological systems and play a significant role in the biofunction of life. These structures are essentially fabricated through the covalent or noncovalent bonds between small chiral molecules. It is thus an important issue to understand how small chiral molecules can form chiral nanostructures. Here, using a series of isomeric nitrocinnamic amide derivatives, we have investigated the self-assembly behavior and the effect of the substituent position as well as the solvent on the formation of chiral nanostructures. It was found that totally different chiral nanostructures were formed due to the different positions of the nitro group on the cinnamic amide. Moreover, it was found that the chiral sense of the self-assembled nanostructures can be regulated by the solvent whereby helicity inversion was observed. This work provides a simple way to regulate the self-assembly pathway via molecular design and choice of solvent for the controlled creation of chiral nanostructures.

Atomic Force Microscopy Imaging Study of Aligning DNA by Dumbbell-like Au-Fe3O4 Magnetic Nanoparticles

Studies on nucleic acid structure and interactions between nucleic acid and its binding molecules are of great importance for understanding and controlling many important biological processes. Atomic force microscopy (AFM) imaging is one of the most efficient methods to disclose the DNA structure and binding modes between DNA and DNA-binding molecules. Long-chain DNA tends to form a random coiled structure, which prevents direct AFM imaging observation of the subtle structure formed by DNA itself or protein binding. Aligning DNA from the random coiled state into the extended state is not only important for applications in DNA nanotechnology but also for elucidating the interaction mechanism between DNA and other molecules. Here, we developed an efficient method based on the magnetic field to align long-chain DNA on a silicon surface. We used AFM imaging to study the alignment of DNA at the single-molecule level, showing that DNA can be stretched and highly aligned by the manipulation of magnetic nanoparticles tethered to one end of DNA and that the aligned DNA can be imaged clearly by AFM. In the absence of the magnetic field, the aligned DNA can relax back to a random coiled state upon rinsing. Such alignment and relaxation can be repeated many times, which provides an efficient method for the manipulation of individual DNA molecules and the investigation of DNA and DNA-binding molecule interactions.

Reversible Photocontrol of DNA Melting by Visible-Light-Responsive F4-Coordinated Azobenzene Compounds

Spatiotemporal control over the regulation of intra- and intermolecular motions in naturally occurring systems is systematically studied to expand the toolbox of mechanical operations in multicomponent nanoarchitectures. DNA is ideally suited for programming light-powered processes that are based on a minimalist molecular design. Here, the noncovalent incorporation of bistable photoswitches into B-like DNA moieties is shown to trigger the thermal transition midpoint of the duplexes by converting visible light into directed mechanical work by orchestrating the collective actions of the photoresponsive chromophores and the host DNA nanostructures. Besides its practical applications, the resulting hybrid nanosystem bears unique features of modulability, biocompatibility, reversibility, and addressability, which are key components for developing molecular photon-controlled programmed materials.

Structuring polarity-inverted TBA to G-quadruplex for selective recognition of planarity of natural isoquinoline alkaloids

Efficient structuring of DNA by small molecules is very crucial in developing DNA-based novel switches with an ideal performance. In this work, we found that inverting only the polarity of the 3' terminal guanine of the thrombin-binding aptamer (3iTBA) totally eradicates the original TBA G-quadruplex (G4) structure in K+. The unstructured 3iTBA can be further refolded upon specifically interacting with small molecules of natural isoquinoline alkaloids (IAs) due to their fruitful binding patterns with variant nucleic acid structures. We identified that 3iTBA can serve as a topology selector for planar IAs. Nitidine (NIT), owing to the planar aromatic ring and coplanar substituents, is the most efficient to restructure the 3iTBA random coil toward the anti-parallel G4 conformation. However, common metal ions can't realize this structuring. The topology selector competency of 3iTBA toward IAs' planarity can be visualized using gold nanoparticles (AuNPs) as the chromogenic readout. Our work expands the G4 repertoire by exploring the polarity inversion regulation and provides a new approach to switch nucleic acid structures toward a small molecule structure-sensitive sensor.

Controlling Supramolecular Chirality in Multicomponent Self-Assembled Systems

Chirality exists as a ubiquitous phenomenon in nature, from molecular level l-amino acids, d-sugar, secondary structures of proteins, DNA, RNA, and nanoscale helices to macroscopic conch and even galaxy. The aggregation of molecular building blocks with or without chiral centers might bring about asymmetric spatial stacking, which further results in the appearance of nonsymmetry in extended scales like helical nanofibers. This phenomenon, known as supramolecular chirality, is an important branch of supramolecular and self-assembly chemistry, which relates intimately with biomimetics, asymmetric catalysis, and designing chiroptic advanced materials. One of the important research focuses among supramolecular chirality is about rational manipulation of chirality amplification and handedness, presenting a profound influence on the performance of resulting soft materials such as circularly polarized luminescence and cell adhesion on hydrogels. The control over supramolecular chirality normally relies on two factors, i.e., thermodynamic and kinetic variables dependent on molecular structural parameters and environmental contributions, respectively. Supramolecular chirality in two or more component-based systems places an emphasis on thermodynamic control as it occurs from either integrated coassembly or separated self-sorting, which is more sophisticated than that of single component systems. Thus, the study on supramolecular chirality in multicomponent systems could mimic complicated biosystems, allowing for better understanding about the origin of natural chirality and extended applications as biomimetics. To date, the exploration of supramolecular chirality in multicomponent systems is restricted on both fundamental and application aspects when compared to more matured single component systems. Over the past few years, we have carried out systematic studies on several systems expressing supramolecular chirality from chiral amplification or symmetry breaking. We emphasized more the thermodynamic control by introducing a second component to form noncovalent bonding like hydrogen bonding or coordination interactions. In this Account, we would specifically discuss rational manipulation of the occurrence, transfer, and inversion of supramolecular chirality by taking several of the latest representative examples. In the multicomponent systems, in addition to the building blocks with chiral centers, the second or third components could be structural analogues and achiral small molecules such as bipyridines, melamine, metal ions, inorganic nanomaterials, and even solvents. These second or third components are able to incorporate during the aggregation to form coassembly via noncovalent bonds, influencing spatial arrangements of building blocks within various dimensions from vesicles and nanofibers to organic/inorganic hybrids. Other than chirality, morphology, stimulus responsiveness, and properties could also be well tailored by controlling interactions between different components.

Twisted bio-nanorods serve as a template for constructing chiroptically active nanoflowers

Using biomacromolecule-based nanorods as a chiral source is a creative way to fabricate broadband chiroptically active nanoarchitectures. Herein, right-handedly twisted cellulose nanocrystal (CNC) nanorods, serving simultaneously as a chiral template and a building block, were combined with CuO for constructing composite nanoflowers that showed broadband chiroptical activity. Through calcination, the CuO/CNC nanoflowers can transform into chiral CuO with a flower-like architecture. The established preparation technology is expected to provide various novel broadband chiroptically active nanoarchitectures originating from CNCs and metal oxides.

Light-driven chiroptical photoswitchable DNA assemblies mediated by bioinspired photoresponsive molecules

We show that the incorporation of chiral bioinspired photochromic compounds into inherently chiral DNA matrices enables the building of smart nanoscale photoswitchable chiroptical assemblies tunable over a wide range of wavelengths. Moreover, the use of light as external trigger affords precise control of the resulting hybrid DNA nanostructures, and their chiroptical activities can be spatially modulated without photochemical fatigue.

Oxazolidine Transient Bases as Molecular Platforms for Testing Dynamic CO2 Capture in Biochemical Systems

Understanding the dynamic processes of CO₂ capture in biosystems is important because of the great effect CO₂ has on the carbon cycle, human health, the global climate, and living environments. After years of multidisciplinary studies, researchers have gained only basic mechanistic knowledge about how enzymes or protein-aggregates capture and deliver CO₂, a process involving reversible bonding of CO₂ with basic amino acid residues. However, vital mechanistic details of how the activated basic residues within these enzymes or protein-aggregates are initially formed, a crucial step for CO₂ capture, are still lacking. Herein, we designed specific molecules, i.e., oxazolidines, which are able to reversibly change their alkalinity via ultrafast isomerizations. Serving as so-called transient bases, these oxazolidines mimic the activated/deactivated states of enzymes or protein-aggregates responsible for dynamic CO₂ capture/release. A detailed mechanism for CO₂ capture, which involves dynamic covalent bonding and multimolecular cooperative interactions among functional groups that occur with the help of a polyhydroxyl environment, is demonstrated by UV-vis and multiple NMR spectroscopies as well as theoretical calculations. Using suitable oxazolidine transient bases, applications for visual CO₂ detection under different detection limit requirements were also developed. Insights for further understanding the process of dynamic CO₂ capture in biosystems are also discussed. This oxazolidine-inspired biomimetic CO₂ capture serves as a platform for the future development of additional biomimicking systems, as well as offers unique perspectives for other complicated life processes.

Assembly–disassembly switching of self-sorted nanotubules forming dynamic 2-D porous heterostructure

Self-sorted tubules and sheets are reversibly merged into 2-D porous heterostructure in response to a pH change.

Helicity Inversion of Supramolecular Hydrogels Induced by Achiral Substituents

Probing the supramolecular chirality of assemblies and controlling their handedness are closely related to the origin of chirality at the supramolecular level and the development of smart materials with desired handedness. However, it remains unclear how achiral residues covalently bonded to chiral amino acids can function in the chirality inversion of supramolecular assemblies. Herein, we report macroscopic chirality and dynamic manipulation of chiroptical activity of hydrogels self-assembled from phenylalanine derivatives, together with the inversion of their handedness achieved solely by exchanging achiral substituents between oligo(ethylene glycol) and carboxylic acid groups. This helicity inversion is mainly induced by distinct stacking mode of the self-assembled building blocks, as collectively confirmed by scanning electron microscopy, circular dichroism, crystallography, and molecular dynamics calculations. Through this straightforward approach, we were able to invert the handedness of helical assemblies by merely exchanging achiral substituents at the terminal of chiral gelators. This work not only presents a feasible strategy to achieve the handedness inversion of helical nanostructures for better understanding of chiral self-assembly process in supramolecular chemistry but also facilities the development of smart materials with controllable handedness in materials science.

Donor-acceptor interaction-driven self-assembly of amphiphilic rod-coil molecules into supramolecular nanoassemblies

Rigid-flexible amphiphilic molecules consisting of an aromatic segment based on pyrene and biphenyl units and hydrophilic polyethylene oxide chains self-assemble into lamellar, hexagonal columnar, and two-dimensional columnar nanostructures in the bulk state. In aqueous solution, these molecules self-assemble into nanofibers, spherical micelles, and multilayer nanotubes, depending on the chain or rod length of the molecules. Notably, ordered nanostructures of supramolecular polymers, such as single-layer curving fragments, nanofibers, and nanosheets, were constructed through charge-transfer interactions between the nanoobjects and an electron-acceptor molecule, 2,4,5,7-tetranitrofluorenone. These experimental results reveal that diverse supramolecular morphologies can be controlled by tuning rod-coil molecular interactions or charge-transfer interactions between the donor and acceptor molecules.

Solvent Dielectricity-Modulated Helical Assembly and Morphologic Transformation of Achiral Surfactant-Inorganic Cluster Ionic Complexes

Ionic complexes comprising single/double chain cationic surfactant and Lindqvist-type polyoxomolybdate anionic cluster were used for controlled self-assembly in organic solutions. In the solvent with low dielectric constant the complexes self-assembled into flat ribbon like lamellar aggregations with an inverse bilayer substructure where the cluster located at the middle. Under the condition of increased dielectric constant, the solvent triggered the formation of helical self-assemblies, which finally transformed from helical ribbons to the flower-like assemblies due to the bilayer becoming excessively twisted. The self-assembled morphology and the substructure were characterized by SEM, TEM, and XRD. The solvent dielectricity-controlled morphologic transformations modulated by the variation of electrostatic interactions between organic cations and inorganic polyanions were demonstrated by ¹H NMR and IR spectra. The strategy in this work represents an effective route in targeting the chirality-directed functionalization of inorganic clusters by combining controllable and helical assemblies of achiral polyoxometalate complexes in one system.

The Helix to Super-Helix Transition in the Self-Assembly of π-Systems: Superseding of Molecular Chirality at Hierarchical Level

Higher-order super-helical structures derived from biological molecules are known to evolve through opposite coiling of the initial helical fibers, as seen in collagen protein. A similar phenomenon is observed in a π-system self-assembly of chiral oligo(phenyleneethylene) derivatives (S)-1 and (R)-1 that explains the unequal formation of both left- and right-handed helices from molecule having a specific chiral center. Concentration- and temperature-dependent circular dichroism (CD) and UV/Vis spectroscopic studies revealed that the initial formation of helical aggregates is in accordance with the molecular chirality. At the next level of hierarchical self-assembly, coiling of the fibers occurs with opposite handedness, thereby superseding the command of the molecular chirality. This was confirmed by solvent-dependent decoiling of super-helical structures and concentration-dependent morphological analysis.