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.

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.

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.

Regulating Spatial Localization and Reactivity Biasness of DNAzymes by Metal Ions and Oligonucleotides.

Chemical gradient sensing behavior of catalytically active colloids and enzymes is an area of immense interest owing to their importance in understanding fundamental spatiotemporal complexity patterns in living systems and designing dynamic materials. Herein, we have shown the peroxidase activity of DNAzyme (G-quadruplex-hemin complex tagged in a micron-sized glass bead) can be modulated by metal ions and metal ion-binding oligonucleotides. Next we demonstrated both experimentally and theoretically, that the localization and product formation ability of the DNAzyme-containing particle remains biased to the more catalytically active zone where the concentration of metal ion (Hg2+ ) inhibitor is low. Interestingly, this biased localization can be broken by introduction of Hg2+ binding oligonucleotide in the system. Additionally, a macroscopically asymmetric catalytic product distributed zone has been achieved with this process, showing the possibility of regulation in autonomous spatially controlled chemical processes. This demonstration of autonomous modulation of the localization pattern and spatially specific enhanced product forming ability of DNAzymes will further enable the design of responsive nucleic acid-based motile materials and surfaces.

Spatiotemporal dynamics of self-assembled structures in enzymatically induced agonistic and antagonistic conditions.

Predicting and designing systems with dynamic self-assembly properties in a spatiotemporal fashion is an important research area across disciplines ranging from understanding the fundamental non-equilibrium features of life to the fabrication of next-generation materials with life-like properties. Herein, we demonstrate a spatiotemporal dynamics pattern in the self-assembly behavior of a surfactant from an unorganized assembly, induced by adenosine triphosphate (ATP) and enzymes responsible for the degradation or conversion of ATP. We report the different behavior of two enzymes, alkaline phosphatase (ALP) and hexokinase (HK), towards adenosine triphosphate (ATP)-driven surfactant assembly, which also results in contrasting spatiotemporal dynamic assembly behavior. Here, ALP acts antagonistically, resulting in transient self-assemblies, whereas HK shows agonistic action with the ability to sustain the assemblies. This dynamic assembly behavior was then used to program the time-dependent emergence of a self-assembled structure in a two-dimensional space by maintaining concentration gradients of the enzymes and surfactant at different locations, demonstrating a new route for obtaining 'spatial' organizational adaptability in a self-organized system of interacting components for the incorporation of programmed functionality.