ATP‐Driven Synthetic Supramolecular Assemblies: From ATP as a Template to Fuel

Persistent ATP-Concentration Gradients in a Hydrogel Sustained by Chemical Fuel Consumption

We show the formation of macroscopic ATP-concentrations in an agarose gel and demonstrate that these gradients can be sustained in time at the expense of the consumption of a chemical fuel. The approach relies on the spatially controlled activation of ATP-producing and ATP-consuming reactions through the local injection of enzymes in the matrix. The reaction-diffusion system is maintained in a stationary non-equilibrium state as long as chemical fuel, phosphocreatine, is present. The reaction-diffusion system is coupled to a supramolecular system composed of monolayer protected gold nanoparticles and a fluorescent probe. As a result of this coupling, fluorescence signals emerge spontaneously in response to the ATP-concentration gradients. We show that the approach permits the rational formation of complex fluorescence patterns that change over time as a function of the evolution of the ATP-concentrations present in the system.

Communication and Cross-Regulation between Chemically Fueled Sender and Receiver Reaction Networks

Nature connects multiple fuel-driven chemical/enzymatic reaction networks (CRNs/ERNs) via cross-regulation to hierarchically control biofunctions for a tailored adaption in complex sensory landscapes. Herein, we introduce a facile example of communication and cross-regulation among two fuel-driven DNA-based ERNs regulated by a concatenated RNA transcription regulator. ERN1 ("sender") is designed for the fuel-driven promoter formation for T7 RNA polymerase, which activates RNA transcription. The produced RNA can deactivate or activate DNA in ERN2 ("receiver") by toehold-mediated strand displacement, leading to a communication between two ERNs. The RNA from ERN1 can repress or promote the fuel-driven state of ERN2; ERN2 in turn feedbacks to regulate the lifetime of ERN1. Furthermore, the incorporation of RNase H allows for RNA degradation and enables the autonomous recovery of ERN2. We believe that concatenation of multiple CRNs/ERNs provides a basis for the design of more elaborate autonomous regulatory mechanisms in systems chemistry and synthetic biology.

Green AOT reverse micelles as nanoreactors for alkaline phosphatase. The hydrogen bond "dances" between water and the enzyme, the reaction product, and the reverse micelles interface

In this work, we present an investigation of the influence of water encapsulated in 1,4-bis-2-ethylhexylsulfosuccinate/methyl laurate and 1,4-bis-2-ethylhexylsulfosuccinate/isopropyl myristate reverse micelles on the enzymatic hydrolysis of 1-naphthyl phosphate by alkaline phosphatase. Our results show that the enzyme is active in the biocompatible reverse micelles studied and that the Michaelis-Menten kinetic model is valid in all systems. We found that both micellar systems studied have a particular behavior toward pH and that the penetration of external solvents into the interfaces is crucial to understanding the effect. Methyl laurate does not disrupt the interface and is not necessary to control the pH value since alkaline phosphatase in the center of the micelles is always solvated similarly. In contrast, isopropyl myristate disrupts the interfaces so that the water and 1-naphthol molecules cannot form hydrogen bond interactions with the polar head of the surfactant. Then, when the water is at pH = 7, the 1-naphthol moves away to the interfaces inhibiting alkaline phosphatase which is not observable when the water is at pH = 10. Our study shows that the concept of pH cannot be used directly in a confined environment. In addition, our research is of great importance in the field of reactions that occur in reverse micelles, catalyzed by enzymes.

Hydrogen-bond-driven supramolecular helical assembly of a coumarin-substituted phthalonitrile derivative: synthesis and in vitro anticancer activity against colorectal adenocarcinoma

Phthalonitrile derivatives are generally reported to crystallize in space groups P21/c and P 1 in the literature. In this study, 7-hydroxy-4,8-dimethyl-3-pentylcoumarin (2) and its phthalonitrile derivative (2d) were crystallized; 2d crystallized in the rare trigonal space group R 3. In the phthalonitrile derivative (2d), weak C—H...O hydrogen-bonding interactions promoted the formation of supramolecular double helices, and these supramolecular P and M double helices came together to form a honeycomb-like architectural motif involving one-dimensional tubular channels. In silico molecular-docking studies were performed to support the experimental processes and the results agree with each other. In vitro studies of compounds 2 and 2d were performed in LoVo colorectal adenocarcinoma and CCD18Co healthy human cell lines using flow cytometry. For compounds 2 and 2d, there was a statistically significant increase (p < 0.001) in both early and late apoptosis with respect to the control in a dose-dependent manner.

Biomacromolecule-Fueled Transient Volume Phase Transition of a Hydrogel

A metabolic cycle-inspired hydrogel which exhibits the biomacromolecule-fueled transient volume phase transition is reported. This hydrogel has the affinity and digestive capacity for a fuel α-poly-L-lysine by incorporating acrylic acid and trypsin. The hydrogel captured fuel and transiently shrank owing to the construction of electrostatic cross-linkages. This process was inherently connected with the digestion of these cross-linkages and the release of oligo-lysine as waste, which induced the reswelling of the hydrogel at equilibrium. The transient volume change of the hydrogel realized the fuel-stimulated transient release of a payload. This study provides a strategy for engineering materials with biomacromolecule-fueled dynamic functions under the out-of-equilibrium condition.

Electrostatically Directed Long-Range Self-Assembly of Nucleotides with Cationic Nanoparticles To Form Multifunctional Bioplasmonic Networks

Precise control over interparticle interactions is essential to retain the functions of individual components in a self-assembled superstructure. Here, we report the design of a multifunctional bioplasmonic network via an electrostatically directed self-assembly process involving adenosine 5'-triphosphate (ATP). The present study unveils the ability of ATP to undergo a long-range self-assembly in the presence of cations and gold nanoparticles (AuNP). Modelling and NMR studies gave a qualitative insight into the major interactions driving the bioplasmonic network formation. ATP-Ca²⁺ coordination helps in regulating the electrostatic interaction, which is crucial in transforming an uncontrolled precipitation into a kinetically controlled aggregation process. Remarkably, ATP and AuNP retained their inherent properties in the multifunctional bioplasmonic network. The generality of electrostatically directed self-assembly process was extended to different nucleotide-nanoparticle systems.

Expanding the Scope of Metastable Species in Hydrogen Bonding‐Directed Supramolecular Polymerization

We reveal unique hydrogen (H‐) bonding patterns and exploit them to control the kinetics, pathways and length of supramolecular polymers (SPs). New bisamide‐containing monomers were designed to elucidate the role of competing intra‐ vs. intermolecular H‐bonding interactions on the kinetics of supramolecular polymerization (SP). Remarkably, two polymerization‐inactive metastable states were discovered. Contrary to previous examples, the commonly assumed intramolecularly H‐bonded monomer does not evolve into intermolecularly H‐bonded SPs via ring opening, but rather forms a metastable dimer. In this dimer, all H‐bonding sites are saturated, either intra‐ or intermolecularly, hampering elongation. The dimers exhibit an advantageous preorganization, which upon opening of the intramolecular portion of the H‐bonding motif facilitates SP in a consecutive process. The retardation of spontaneous self‐assembly as a result of two metastable states enables length control in SP by seed‐mediated growth.

Dissipative Organization of DNA Oligomers for Transient Catalytic Function

The development of synthetic non-equilibrium systems opens doors for man-made life-like materials. Yet, creating distinct transient functions from artificial fuel-driven structures remains a challenge. Building on our ATP-driven dynamic covalent DNA assembly in an enzymatic reaction network of concurrent ATP-powered ligation and restriction, we introduce ATP-fueled transient organization of functional subunits for various functions. The programmability of the ligation/restriction site allows to precisely organize multiple sticky-end-encoded oligo segments into double-stranded (ds) DNA complexes. We demonstrate principles of ATP-driven organization into sequence-defined oligomers by sensing barcode-embedded targets with different defects. Furthermore, ATP-fueled DNAzymes for substrate cleavage are achieved by transiently ligating two DNAzyme subunits into a dsDNA complex, rendering ATP-fueled transient catalytic function.

Chemically Fueled Self-Assembly in Biology and Chemistry

Life is a non-equilibrium state of matter maintained at the expense of energy. Nature uses predominantly chemical energy stored in thermodynamically activated, but kinetically stable, molecules. These high-energy molecules are exploited for the synthesis of other biomolecules, for the activation of biological machinery such as pumps and motors, and for the maintenance of structural order. Knowledge of how chemical energy is transferred to biochemical processes is essential for the development of artificial systems with life-like processes. Here, we discuss how chemical energy can be used to control the structural organization of organic molecules. Four different strategies have been identified according to a distinguishable physical-organic basis. For each class, one example from biology and one from chemistry are discussed in detail to illustrate the practical implementation of each concept and the distinct opportunities they offer. Specific attention is paid to the discussion of chemically fueled non-equilibrium self-assembly. We discuss the meaning of non-equilibrium self-assembly, its kinetic origin, and strategies to develop synthetic non-equilibrium systems.

Tricomponent Supramolecular Multiblock Copolymers with Tunable Composition via Sequential Seeded Growth

Synthesis of supramolecular block co-polymers (BCP) with small monomers and predictive sequence requires elegant molecular design and synthetic strategies. Herein we report the unparalleled synthesis of tri-component supramolecular BCPs with tunable microstructure by a kinetically controlled sequential seeded supramolecular polymerization of fluorescent π-conjugated monomers. Core-substituted naphthalene diimide (cNDI) derivatives with different core substitutions and appended with β-sheet forming peptide side chains provide perfect monomer design with spectral complementarity, pathway complexity and minimal structural mismatch to synthesize and characterize the multi-component BCPs. The distinct fluorescent nature of various cNDI monomers aids the spectroscopic probing of the seeded growth process and the microscopic visualization of resultant supramolecular BCPs using Structured Illumination Microscopy (SIM). Kinetically controlled sequential seeded supramolecular polymerization presented here is reminiscent of the multi-step synthesis of covalent BCPs via living chain polymerization. These findings provide a promising platform for constructing unique functional organic heterostructures for various optoelectronic and catalytic applications.

The Transient Covalent Bond in Abiotic Nonequilibrium Systems

Biochemical systems accomplish many critical functions with by operating out-of-equilibrium using the energy of chemical fuels. The formation of a transient covalent bond is a simple but very effective tool in designing analogous reaction networks. This Minireview focuses on the fuel chemistries that have been used to generate transient bonds in recent demonstrations of abiotic nonequilibrium systems (i.e., systems that do not make use of biological components). Fuel reactions are divided into two fundamental classifications depending on whether the fuel contributes structural elements to the activated state, a distinction that dictates how they can be used. Reported systems are further categorized by overall fuel reaction (e.g., hydrolysis of alkylating agents, carbodiimide hydration) and illustrate how similar chemistry can be used to effect a wide range of nonequilibrium behavior, ranging from self-assembly to the operation of molecular machines.