Synthesis and materialization of a reaction–diffusion French flag pattern

Abstract

During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. First, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically distinct zones with sharp borders whose synthetic analogue has remained elusive. A bistable network within a shallow concentration gradient creates an immobile, sharp and long-lasting concentration front through a reaction-diffusion mechanism. The combination of two bistable circuits generates a French flag pattern whose 'phenotype' can be reprogrammed by network mutation. Second, these concentration patterns control the macroscopic organization of DNA-decorated particles, inducing a French flag pattern of colloidal aggregation. This experimental framework could be used to test reaction-diffusion models and fabricate soft materials following an autonomous developmental programme.

Establishing Communication Between Artificial Cells

“…For instance, as imilars ender-receiver system was later employed to create artificial cells that were able to communicate with live bacterial cells, [32] somewhat remindingo fT uring's classical test for artificial intelligence. [19,33] Meanwhile, various groups reported communication between either identical or distinct types of artificial cells in aw ide variety of settings.E xamples include severals ender-receiver-types ystems, [32b, c] the realization of spatially distributed dynamics, [5,6,11] simple types of spatial differentiation in colloidal materials [8] and tissue-like droplet assemblies. [1] Recently,D NA-functionalized gel particlesw ere encapsulated within larger compartments as primitive mimics of eukaryotic cells with an ucleus and organelles, [9,12] and communication was demonstrated among particles within as ingle compartment, [9] and also between the eukaryotic cell mimics.…”

“…For instance, proteins weree xchanged between chip-based compartments [5,6] and semipermeable clay hydrogels. [12] Quite recently,e ven nucleic acids were utilized as "programmable" signaling molecules for communicating artificial cell-like compartments.I nt hese cases, they were either exchanged between DNA modified polymerb eads, [8] functionalized gel particles with large pores, [9] or proteinosomes. [17]…”

“…[78] Later,Z adorin et al used the PEN toolboxt og enerate1 DD NA concentrationp atterns in ar eactionc hamber. [8] By using DNA molecules as cross-linkers for microbeads, they were able to transfer the continuous pattern into am aterialized pattern of cross-linking density. More recently,D upin and Simmel have realized as imple form of differentiation among nominally identical receiver cells connected to as ingle sender cell.…”

Artificial Gel‐Based Organelles for Spatial Organization of Cell‐Free Gene Expression Reactions

“…Among other applications, such systems were used to engineer biochemical reaction networks that exhibit a variety of spatial patterns and wave-like dynamics [7, 10] , or to mimic predatory behavior [11] .…”

Künstliche, gelbasierte Organellen für die räumliche Organisation von zellfreien Genexpressionsreaktionen

“…In diesem Zusammenhang wurden zuletzt membranfreie Kompartimente wie chipbasierte Genexpressionssysteme, [9] Mikrokügelchen, [10] Koazervate [11] oder Hydrogele [12] fürd ie Realisierung dynamischer Systeme mit diffundierenden Nukleinsäuresignalen verwendet. Zusätzlich zu anderen Anwendungen wurden mit solchen Systemen auch biochemische Reaktionsnetzwerke realisiert, die räumliche Muster oder wellenartige Dynamik generieren [10,13] oder auch Jäger-Beute-Dynamik imitieren konnten. [14] Hier entwickeln wir ein Verfahren fürd ie kovalente Immobilisierung von DNA-Molekülen von der Länge ganzer Gene in Agarose-Mikrogelkügelchen und demonstrieren deren Kompatibilitätm it In-vitro-Transkription (IVT) und zellfreier Proteinexpression (ZFPE).…”