DNA-Controlled Spatiotemporal Patterning of a Cytoskeletal Active Gel

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.

Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller

In recent years, there has been a growing interest in engineering dynamic and autonomous systems with robotic functionalities using biomolecules. Specifically, the ability of molecular motors to convert chemical energy to mechanical forces and the programmability of DNA are regarded as promising components for these systems. However, current systems rely on the manual addition of external stimuli, limiting the potential for autonomous molecular systems. Here, we show that DNA-based cascade reactions can act as a molecular controller that drives the autonomous assembly and disassembly of DNA-functionalized microtubules propelled by kinesins. The DNA controller is designed to produce two different DNA strands that program the interaction between the microtubules. The gliding microtubules integrated with the controller autonomously assemble to bundle-like structures and disassemble into discrete filaments without external stimuli, which is observable by fluorescence microscopy. We believe this approach to be a starting point toward more autonomous behavior of motor protein-based multicomponent systems with robotic functionalities.

Pumping Small Molecules Selectively through an Energy-Assisted Assembling Process at Nonequilibrium States

In living organisms, precise control over the spatial and temporal distribution of molecules, including pheromones, is crucial. This level of control is equally important for the development of artificial active materials. In this study, we successfully controlled the distribution of small molecules in the system at nonequilibrium states by actively transporting them, even against the apparent concentration gradient, with high selectivity. As a demonstration, in the aqueous solution of acid orange (AO7) and TMC10COOH, we found that AO7 molecules can coassemble with transient anhydride (TMC10CO)2O to form larger assemblies in the presence of chemical fuel 1-ethyl-3-(3-(dimethylamino)propyl) carbodiimide hydrochloride (EDC). This led to a decrease in local free AO7 concentration and caused AO7 molecules from other locations in the solution to move toward the assemblies. Consequently, AO7 accumulates at the location where EDC was injected. By continuously injecting EDC, we could maintain a stable high value of the apparent AO7 concentration at the injection point. We also observed that this process which operated at nonequilibrium states exhibited high selectivity.

Building on-chip cytoskeletal circuits via branched microtubule networks

Controllable platforms to engineer robust cytoskeletal scaffolds have the potential to create novel on-chip nanotechnologies. Inspired by axons, we combined the branching microtubule (MT) nucleation pathway with microfabrication to develop "cytoskeletal circuits." This active matter platform allows control over the adaptive self-organization of uniformly polarized MT arrays via geometric features of microstructures designed within a microfluidic confinement. We build and characterize basic elements, including turns and divisions, as well as complex regulatory elements, such as biased division and MT diodes, to construct various MT architectures on a chip. Our platform could be used in diverse applications, ranging from efficient on-chip molecular transport to mechanical nano-actuators. Further, cytoskeletal circuits can serve as a tool to study how the physical environment contributes to MT architecture in living cells.

Functional Nucleic Acid Probes Based on Two-Photon for Biosensing

Functional nucleic acid (FNA) probes have been widely used in environmental monitoring, food analysis, clinical diagnosis, and biological imaging because of their easy synthesis, functional modification, flexible design, and stable properties. However, most FNA probes are designed based on one-photon (OP) in the ultraviolet or visible regions, and the effectiveness of these OP-based FNA probes may be hindered by certain factors, such as their potential for photodamage and limited light tissue penetration. Two-photon (TP) is characterized by the nonlinear absorption of two relatively low-energy photons of near-infrared (NIR) light with the resulting emission of high-energy ultraviolet or visible light. TP-based FNA probes have excellent properties, including lower tissue self-absorption and autofluorescence, reduced photodamage and photobleaching, and higher spatial resolution, making them more advantageous than the conventional OP-based FNA probes in biomedical sensing. In this review, we summarize the recent advances of TP-excited and -activated FNA probes and detail their applications in biomolecular detection. In addition, we also share our views on the highlights and limitations of TP-based FNA probes. The ultimate goal is to provide design approaches for the development of high-performance TP-based FNA probes, thereby promoting their biological applications.

In Vitro Synthesis and Design of Kinesin Biomolecular Motors by Cell-Free Protein Synthesis

Kinesin is a biomolecular motor that generates force and motility along microtubule cytoskeletons in cells. Owing to their ability to manipulate cellular nanoscale components, microtubule/kinesin systems show great promise as actuators of nanodevices. However, classical in vivo protein production has some limitations for the design and production of kinesins. Designing and producing kinesins is laborious, and conventional protein production requires specific facilities to create and contain recombinant organisms. Here, we demonstrated the in vitro synthesis and editing of functional kinesins using a wheat germ cell-free protein synthesis system. The synthesized kinesins propelled microtubules on a kinesin-coated substrate and showed a higher binding affinity with microtubules than E. coli-produced kinesins. We also successfully incorporated affinity tags into the kinesins by extending the original sequence of the DNA template by PCR. Our method will accelerate the study of biomolecular motor systems and encourage their wider use in various nanotechnology applications.

Self-mixing in microtubule-kinesin active fluid from nonuniform to uniform distribution of activity

Active fluids have applications in micromixing, but little is known about the mixing kinematics of systems with spatiotemporally-varying activity. To investigate, UV-activated caged ATP is used to activate controlled regions of microtubule-kinesin active fluid and the mixing process is observed with fluorescent tracers and molecular dyes. At low Péclet numbers (diffusive transport), the active-inactive interface progresses toward the inactive area in a diffusion-like manner that is described by a simple model combining diffusion with Michaelis-Menten kinetics. At high Péclet numbers (convective transport), the active-inactive interface progresses in a superdiffusion-like manner that is qualitatively captured by an active-fluid hydrodynamic model coupled to ATP transport. Results show that active fluid mixing involves complex coupling between distribution of active stress and active transport of ATP and reduces mixing time for suspended components with decreased impact of initial component distribution. This work will inform application of active fluids to promote micromixing in microfluidic devices.

In situ integrated microrobots driven by artificial muscles built from biomolecular motors

Microrobots have been developed for applications in the submillimeter domain such as the manipulation of micro-objects and microsurgery. Rapid progress has been achieved in developing miniaturized components for microrobotic systems, resulting in a variety of functional microactuators and soft components for creating untethered microrobots. Nevertheless, the integration of microcomponents, especially the assembly of actuators and mechanical components, is still time-consuming and has inherent restrictions, thus limiting efficient fabrications of microrobots and their potential applications. Here, we propose a method for fabricating microrobots in situ inspired by the construction of microsystems in living organisms. In a microfluidic chip, hydrogel mechanical components and artificial muscle actuators are successively photopatterned from hydrogel prepolymer and biomolecular motors, respectively, and integrated in situ into functional microrobots. The proposed method allows the fast fabrication of microrobots through simple operations and affordable materials while providing versatile functions through the precise spatiotemporal control of in situ integration and reconfiguration of artificial muscles. To validate the method, we fabricated microrobots to elicit different motions and on-chip robots with unique characteristics for microfluidic applications. This study may establish a new paradigm for microrobot integration and lead to the production of unique biohybrid microrobots with various advantages.

Crosslinking and depletion determine spatial instabilities in cytoskeletal active matter

Active gels made of cytoskeletal proteins are valuable materials with attractive non-equilibrium properties such as spatial self-organization and self-propulsion. At least four typical routes to spatial patterning have been reported to date in different types of cytoskeletal active gels: bending and buckling instabilities in extensile systems, and global and local contraction instabilities in contractile gels. Here we report the observation of these four instabilities in a single type of active gel and we show that they are controlled by two parameters: the concentrations of ATP and depletion agent. We demonstrate that as the ATP concentration decreases, the concentration of passive motors increases until the gel undergoes a gelation transition. At this point, buckling is selected against bending, while global contraction is favored over local ones. Our observations are coherent with a hydrodynamic model of a viscoelastic active gel where the filaments are crosslinked with a characteristic time that diverges as the ATP concentration decreases. Our work thus provides a unified view of spatial instabilities in cytoskeletal active matter.

Front speed and pattern selection of a propagating chemical front in an active fluid

Spontaneous pattern formation in living systems is driven by reaction-diffusion chemistry and active mechanics. The feedback between chemical and mechanical forces is often essential to robust pattern formation, yet it remains poorly understood in general. In this analytical and numerical paper, we study an experimentally motivated minimal model of coupling between reaction-diffusion and active matter: a propagating front of an autocatalytic and stress-generating species. In the absence of activity, the front is described by the well-studied Kolmogorov, Petrovsky, and Piskunov equation. We find that front propagation is maintained even in active systems, with crucial differences: an extensile stress increases the front speed beyond a critical magnitude of the stress, while a contractile stress has no effect on the front speed but can generate a periodic instability in the high-concentration region behind the front. We expect our results to be useful in interpreting pattern formation in active systems with mechanochemical coupling in vivo and in vitro.