Cascaded pattern formation in hydrogel medium using the polymerisation approach

Abe, K.; Murata, Satoshi; Kawamata, Ibuki

doi:10.1039/d1sm00296a

Cited by 3 publications

(3 citation statements)

References 47 publications

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“…DNA is among the versatile materials for building molecular architectures (13)(14)(15)(16)(17)(18) and designing chemical cascades (19)(20)(21)(22) owing to its ability to arbitrarily tune the reactivity to other DNA by designing the sequences of its building units. Several attempts have been made to develop DNA-based molecular systems with dynamic robotic functionalities, such as assembly lines, autonomous molecular crawling, and reversible cumulative actuation (23-25).…”

Section: Introductionmentioning

confidence: 99%

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

Kawamata,

Nishiyama,

Matsumoto

et al. 2024

Sci. Adv.

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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.

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Section: Introductionmentioning

confidence: 99%

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

Kawamata,

Nishiyama,

Matsumoto

et al. 2024

Sci. Adv.

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“…Dupin et al implemented simple forms of symmetry breaking or stripe formation within assemblies of emulsion droplets that contained feedback gene circuits operated in bacterial cell extract. Notably, reaction-diffusion systems were also realized in enzyme-free systems exclusively based on DNA strand displacement reactions. − …”

Section: Introductionmentioning

confidence: 99%

Steady-State Operation of a Cell-Free Genetic Band-Detection Circuit

2022

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Pattern formation processes play a decisive role during embryogenesis and involve the precise spatial and temporal orchestration of intricate gene regulatory processes. Synthetic gene circuits modeled after their biological counterparts can be used to investigate such processes under well-controlled conditions and may, in the future, be utilized for autonomous position determination in synthetic biological materials. Here, we investigated a three-node feed-forward gene regulatory circuit in vitro that generates three distinct fluorescent outputs in response to varying concentrations of a single externally supplied morphogen. The circuit acts as a band detector for the morphogen concentration and, in a spatial context, could serve as a stripe-forming gene circuit. We simulated the behavior of the genetic circuit in the presence of a morphogen gradient using a system of ordinary differential equations and determined optimal parameters for stripe-pattern formation using an evolutionary algorithm. To analyze the subcircuits of the system, we conducted cell-free characterization experiments and finally tested the whole genetic circuit in nanoliter-scale microfluidic flow reactors that provided a continuous supply of cell extract and metabolites and allowed removal of degradation products. To make use of the widely employed promoters PLlacO‑1 and PLtetO‑1 in our design, we removed LacI from our bacterial cell extract by genome engineering Escherichia coli using a pORTMAGE workflow. Our results show that the band-detector works as designed when operated out of equilibrium within the flow reactors. On the other hand, subcircuits of the system and the whole circuit fail to generate the desired gene expression response when operated in a closed reactor. Our work thus underlines the importance of out-of-equilibrium operation of complex gene circuits, which cannot settle to a steady-state expression pattern within the finite lifetime of a cell-free expression system.

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“…Despite its importance in the development of life-like synthetic materials, , engineering such a chemomechanical trigger remains challenging. An important body of work has developed methods to chemically actuate hydrogels; , however, the current approaches either pattern passive hydrogels − or trigger deformations in active gels with chemical reactions that are difficult to design. , …”

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confidence: 99%

DNA-Controlled Spatiotemporal Patterning of a Cytoskeletal Active Gel

2021

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Living cells move and change their shape because signaling chemical reactions modify the state of their cytoskeleton, an active gel that converts chemical energy into mechanical forces. To create life-like materials, it is thus key to engineer chemical pathways that drive active gels. Here we describe the preparation of DNA-responsive surfaces that control the activity of a cytoskeletal active gel composed of microtubules: A DNA signal triggers the release of molecular motors from the surface into the gel bulk, generating forces that structure the gel. Depending on the DNA sequence and concentration, the gel forms a periodic band pattern or contracts globally. Finally, we show that the structuration of the active gel can be spatially controlled in the presence of a gradient of DNA concentration. We anticipate that such DNA-controlled active matter will contribute to the development of life-like materials with self-shaping properties.

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Cascaded pattern formation in hydrogel medium using the polymerisation approach

Abstract: A novel reaction-diffusion system utilizing two-segment DNA polymerisation is proposed. Produced pattern is immobilised in a hydrogel medium, which enables cascaded reaction for further pattern formation.

Cited by 3 publications

References 47 publications

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

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

Steady-State Operation of a Cell-Free Genetic Band-Detection Circuit

DNA-Controlled Spatiotemporal Patterning of a Cytoskeletal Active Gel

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