The enzyme-free catalytic hairpin assembly (CHA) process is introduced as a functional reaction module for guided, high-throughput, emergence, and evolution of constitutional dynamic networks, CDNs, from a set of nucleic acids. The process is applied to assemble networks of variable complexities, functionalities, and spatial confinement, and the systems provide possible mechanistic pathways for the evolution of dynamic networks under prebiotic conditions. Subjecting a set of four or six structurally engineered hairpins to a promoter P₁ leads to the CHA-guided emergence of a [2 × 2] CDN or the evolution of a [3 × 3] CDN, respectively. Reacting of a set of branched three-arm DNA-hairpin-functionalized junctions to the promoter strand activates the CHA-induced emergence of a three-dimensional (3D) CDN framework emulating native gene regulatory networks. In addition, activation of a two-layer CHA cascade circuit or a cross-catalytic CHA circuit and cascaded driving feedback-driven evolution of CDNs are demonstrated. Also, subjecting a four-hairpin-modified DNA tetrahedron nanostructure to an auxiliary promoter strand simulates the evolution of a dynamically equilibrated DNA tetrahedron-based CDN that undergoes secondary fueled dynamic reconfiguration. Finally, the effective permeation of DNA tetrahedron structures into cells is utilized to integrate the four-hairpin-functionalized tetrahedron reaction module into cells. The spatially localized miRNA-triggered CHA evolution and reconfiguration of CDNs allowed the logic-gated imaging of intracellular RNAs. Beyond the bioanalytical applications of the systems, the study introduces possible mechanistic pathways for the evolution of functional networks under prebiotic conditions.

中文翻译：

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无酶催化 DNA 电路驱动的级联、反馈驱动和空间局部化构成动态网络的出现

无酶催化发夹组装（CHA）过程作为功能反应模块被引入，用于从一组核酸引导、高通量、出现和进化组成动态网络（CDN）。该过程用于组装具有可变复杂性、功能和空间限制的网络，并且该系统为生命起源条件下动态网络的进化提供了可能的机制途径。将一组四个或六个结构工程发夹置于启动子 P _1下分别导致 CHA 引导下 [2 × 2] CDN 的出现或 [3 × 3] CDN 的演化。一组分支三臂 DNA 发夹功能化连接与启动子链的反应激活了 CHA 诱导的模拟天然基因调控网络的三维 (3D) CDN 框架的出现。此外，还演示了两层 CHA 级联电路或交叉催化 CHA 电路的激活以及 CDN 的级联驱动反馈驱动演化。此外，将四发夹修饰的 DNA 四面体纳米结构置于辅助启动子链下，模拟了动态平衡的基于 DNA 四面体的 CDN 的演化，该 CDN 经历了二次燃料动态重构。最后，利用DNA四面体结构对细胞的有效渗透，将四发夹功能化的四面体反应模块整合到细胞中。空间定位的 miRNA 触发的 CHA 进化和 CDN 的重新配置允许细胞内 RNA 的逻辑门控成像。除了系统的生物分析应用之外，该研究还介绍了生命起源条件下功能网络进化的可能机制途径。