Efforts to construct synthetic biological circuits with more complex functions have often been hindered by the idiosyncratic behavior, limited dynamic range and crosstalk of commonly utilized parts. Here, we employ de novo RNA design to develop two high-performance translational repressors with sensing and logic capabilities. These synthetic riboregulators, termed toehold repressors and three-way junction (3WJ) repressors, detect transcripts with nearly arbitrary sequences, repress gene expression by up to 300-fold and yield orthogonal sets of up to 15 devices. Automated forward engineering is used to improve toehold repressor dynamic range and SHAPE-Seq is applied to confirm the designed switching mechanism of 3WJ repressors in living cells. We integrate the modular repressors into biological circuits that execute universal NAND and NOR logic and evaluate the four-input expression NOT ((A1 AND A2) OR (B1 AND B2)) in Escherichia coli. These capabilities make toehold and 3WJ repressors valuable new tools for biotechnological applications.

中文翻译：

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从头设计的用于多输入细胞逻辑的翻译抑制核糖调节器。

构建具有更复杂功能的合成生物电路的努力经常受到常用部件的特殊行为、有限的动态范围和串扰的阻碍。在这里，我们采用从头 RNA 设计来开发两种具有传感和逻辑能力的高性能翻译抑制因子。这些合成 riboregulators，称为 toehold 阻遏物和三向连接 (3WJ) 阻遏物，可检测具有几乎任意序列的转录本，将基因表达抑制多达 300 倍，并产生多达 15 个设备的正交组。自动正向工程用于改善立足点阻遏物的动态范围，并应用 SHAPE-Seq 来确认活细胞中 3WJ 阻遏物的设计切换机制。我们将模块化阻遏物集成到执行通用 NAND 和 NOR 逻辑的生物电路中，并评估大肠杆菌中的四输入表达式 NOT ((A1 AND A2) OR (B1 AND B2))。这些功能使 toehold 和 3WJ 阻遏物成为生物技术应用的宝贵新工具。