Interconnectivity between Surface Reactivity and Self-Assembly of Kemp Elimination Catalyzing Nanorods

Enzymatic Dissociation of DNA-Histone Condensates in an Electrophoretic Setting: Modulating DNA Patterning and Hydrogel Viscoelasticity

Development of an energy-driven self-assembly process is a matter of interest for understanding and mimicking diverse ranges of biological and environmental patterns in a synthetic system. In this article, first we demonstrate transient and temporally controlled self-assembly of a DNA-histone condensate where trypsin (already present in the system) hydrolyzes histone, resulting in disassembly. Upon performing this dynamic self-assembly process in a gel matrix under an electric field, we observe diverse kinds of DNA patterning across the gel matrix depending on the amount of trypsin, incubation time of the reaction mixture, and gel porosity. Notably, here, the micrometer-sized DNA-histone condensate does not move through the gel and only free DNA can pass; therefore, transport and accumulation of DNA at different zones depend on the release rate of DNA by trypsin. Furthermore, we show that the viscoelasticity of the native gel increases in the presence of DNA and a pattern over gel viscoelasticity at different zones can be achieved by tuning the amount of enzyme, i.e., the dissociation rate of the DNA-histone condensate. We believe enabling spatiotemporally controlled DNA patterning by applying an electric field will be potentially important in designing different kinds of spatiotemporally distinct dynamic materials.

In situ enzymatic control of colloidal phoresis and catalysis through hydrolysis of ATP

The ability to sense chemical gradients and respond with directional motility and chemical activity is a defining feature of complex living systems. There is a strong interest among scientists to design synthetic systems that emulate these properties. Here, we realize and control such behaviors in a synthetic system by tailoring multivalent interactions of adenosine nucleotides with catalytic microbeads. We first show that multivalent interactions of the bead with gradients of adenosine mono-, di- and trinucleotides (AM/D/TP) control both the phoretic motion and a proton-transfer catalytic reaction, and find that both effects are diminished greatly with increasing valence of phosphates. We exploit this behavior by using enzymatic hydrolysis of ATP to AMP, which downregulates multivalent interactivity in situ. This produces a sudden increase in transport of the catalytic microbeads (a phoretic jump), which is accompanied by increased catalytic activity. Finally, we show how this enzymatic activity can be systematically tuned, leading to simultaneous in situ spatial and temporal control of the location of the microbeads, as well as the products of the reaction that they catalyze. These findings open up new avenues for utilizing multivalent interaction-mediated programming of complex chemo-mechanical behaviors into active systems.

Transient Metallo-Lipidoid Assemblies Amplify Covalent Catalysis of Aqueous and Non-Aqueous Reactions

Dissipative supramolecular assemblies are hallmarks of living systems, contributing to their complex, dynamic structures and emerging functions. Living cells can spatiotemporally control diverse biochemical reactions in membrane compartments and condensates, regulating metabolite levels, signal transduction or remodeling of the cytoskeleton. Herein, we constructed membranous compartments using self-assembly of lipid-like amphiphiles (lipidoid) in aqueous medium. The new double-tailed lipidoid features Cu(II) coordinated with a tetravalent chelator that dictates the binding of two amphiphilic ligands in cis-orientation. Hydrophobic interactions between the lipidoids coupled with intermolecular hydrogen bonding led to a well-defined bilayer vesicle structure. Oil-soluble SNAr reaction is efficiently upregulated in the hydrophobic cavity, acting as a catalytic crucible. The modular system allows easy incorporation of exposed primary amine groups, which augments the catalysis of retro aldol and C-N bond formation reactions. Moreover, a higher-affinity chelator enables consumption of the Cu(II) template leveraging the differential thermodynamic stability, which allows a controllable lifetime of the vesicular assemblies. Concomitant temporal upregulation of the catalytic reactions could be tuned by the metal ion concentration. This work offers new possibilities for metal ion-mediated dynamic supramolecular systems, opening up a massive repertoire of functionally active dynamic "life-like" materials.

Enzyme-Mediated Temporal Control over the Conformational Disposition of a Condensed Protein in Macromolecular Crowded Media

Temporal regulation between input and output signals is one of the hallmarks of complex biological processes. Herein, we report that the conformational disposition of a protein in macromolecularly crowded media can be controlled with time using enzymes. First, we demonstrate the pH dependence of bovine serum albumin (BSA) condensation and conformational alteration in the presence of poly(ethylene glycol) as a crowder. However, by exploiting the strength of pH-modulatory enzymatic reactions (glucose oxidase and urease), the conversion time between the condensed and free forms can be tuned. Additionally, we demonstrate that the trapping of intermediate states with respect to the overall system at a particular α-helix or β-sheet composition and rotational mobility can be possible simply by altering the substrate concentration. Finally, we show that the intrinsic catalytic ability of BSA toward the Kemp elimination (KE) reaction is inhibited in the aggregated form but regained in the free form. In fact, the rate of KE reaction can also be actuated enzymatically in a temporal fashion, therefore demonstrating the programmability of a cascade of biochemical events in crowded media.

Benchmarking Cationic Monolayer Protected Nanoparticles and Micelles for Phosphate-Mediated and Nucleotide-Selective Proton Transfer Catalysis

Both micelles and self-assembled monolayer (SAM)-protected nanoparticles are capable of efficiently hosting water-immiscible substrates to carry out organic reactions in aqueous media. Herein, we have analyzed the different catalytic effect of SAM-protected cationic nanoparticles and cationic surfactants of varying chain length towards base-catalyzed proton transfer mediated ring-opening reaction of 5-nitrobenzisoxazole (NBI) (also known as Kemp Elimination (KE) reaction). We use inorganic phosphate ion or different nucleotide (phosphate-ligated different nucleoside) as base to promote the reaction on micellar or nanoparticle interface. We find almost 2-3 orders of magnitude higher concentration of surfactants of comparable hydrophobicity required to reach the similar activity which attained by low cationic head group concentration bound on nanoparticle. Additionally, at low concentration of nanoparticle-bound surfactant or with high surfactant in micellar form, nucleotide-selectivity has been observed in activating KE reaction unlike free surfactant at low concentration. Finally, we showed enzyme-mediated nucleotide hydrolysis to generate phosphate ion which in situ upregulate the KE activity much more in GNP-based system compared to CTAB. Notably, we show a reasonable superiority of SAM-protected nanoparticles in activating chemical reaction in micromolar concentration of headgroup which certainly boost up application of SAM-based nanoparticles not only for selective recognition but also as eco-friendly catalyst.

Nanoparticle Self-Assembly: From Design Principles to Complex Matter to Functional Materials

The creation of matter with varying degrees of complexities and desired functions is one of the ultimate targets of self-assembly. The ability to regulate the complex interactions between the individual components is essential in achieving this target. In this direction, the initial success of controlling the pathways and final thermodynamic states of a self-assembly process is promising. Despite the progress made in the field, there has been a growing interest in pushing the limits of self-assembly processes. The main inception of this interest is that the intended self-assembled state, with varying complexities, may not be "at equilibrium (or at global minimum)", rendering free energy minimization unsuitable to form the desired product. Thus, we believe that a thorough understanding of the design principles as well as the ability to predict the outcome of a self-assembly process is essential to form a collection of the next generation of complex matter. The present review highlights the potent role of finely tuned interparticle interactions in nanomaterials to achieve the preferred self-assembled structures with the desired properties. We believe that bringing the design and prediction to nanoparticle self-assembly processes will have a similar effect as retrosynthesis had on the logic of chemical synthesis. Along with the guiding principles, the review gives a summary of the different types of products created from nanoparticle assemblies and the functional properties emerging from them. Finally, we highlight the reasonable expectations from the field and the challenges lying ahead in the creation of complex and evolvable matter.

Perpetuating enzymatically induced spatiotemporal pH and catalytic heterogeneity of a hydrogel by nanoparticles

The attainment of spatiotemporally inhomogeneous chemical and physical properties within a system is gaining attention across disciplines due to the resemblance to environmental and biological heterogeneity. Notably, the origin of natural pH gradients and how they have been incorporated in cellular systems is one of the most important questions in understanding the prebiotic origin of life. Herein, we have demonstrated a spatiotemporal pH gradient formation pattern on a hydrogel surface by employing two different enzymatic reactions, namely, the reactions of glucose oxidase (pH decreasing) and urease (pH increasing). We found here a generic pattern of spatiotemporal change in pH and proton transfer catalytic activity that was completely altered in a cationic gold nanoparticle containing hydrogel. In the absence of nanoparticles, the gradually generated macroscopic pH gradient slowly diminished with time, whereas the presence of nanoparticles helped to perpetuate the generated gradient effect. This behavior is due to the differential responsiveness of the interface of the cationic nanoparticle in temporally changing surroundings with increasing or decreasing pH or ionic contents. Moreover, the catalytic proton transfer ability of the nanoparticle showed a concerted kinetic response following the spatiotemporal pH dynamics in the gel matrix. Notably, this nanoparticle-driven spatiotemporally resolved gel matrix will find applicability in the area of the membrane-free generation and control of spatially segregated chemistry at the macroscopic scale.