Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Department of Physics, University of Chicago, Chicago, IL, USA.
Nat Chem. 2022 Nov;14(11):1224-1232. doi: 10.1038/s41557-022-01001-3. Epub 2022 Aug 4.
Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network's various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.
工程化远离平衡的合成化学网络可以响应环境信号脉冲或切换状态，从而精确调节化学合成或自组装的动力学。目前，这些网络必须经过广泛调整，以补偿网络各种化学组分之间的不同活性和意外反应。具有标准化性能的模块化元件可用于快速构建具有设计功能的网络。在这里，我们开发了标准化的可兴奋化学调节元件，称为基因片段，并使用它们构建复杂的体外转录网络。我们开发了一种鉴定 >15 个具有统一性能和最小串扰的可互换基因片段元件的方案。这些元件可以组合成工程化的前馈和反馈模块，其动力学与简单的动力学模型预测的相匹配。然后可以合理地将模块集成并组织成产生可调谐时间脉冲并充当多态可切换存储器的网络。标准化的基因片段元件，以及识别更多元件的工作流程，应该使工程化复杂的远离平衡化学动力学成为常规。
