利用反义RNA反馈调节遗传逻辑门中的超敏感性
Tuning Ultrasensitivity in Genetic Logic Gates Using Antisense RNA Feedback.
作者信息
Engelmann Nicolai, Molderings Maik, Koeppl Heinz
机构信息
Department of Electrical Engineering and Information Technology, TU Darmstadt, Darmstadt 64283, Germany.
Graduate School Life Science Engineering, TU Darmstadt, Darmstadt 64283, Germany.
出版信息
ACS Synth Biol. 2025 May 16;14(5):1425-1436. doi: 10.1021/acssynbio.4c00438. Epub 2025 May 7.
Inverting genetic logic gates fueled by transcriptional repression is an established building block in genetic circuit design. Often, the gates' dose-response curves require large changes in dose to transition between logic ON and OFF states, potentially leading to logically indeterminate intermediate states when gates are connected. Additionally, leakage in the OFF state is a general concern, especially at the output stages of a circuit. This study explores the potential to improve inverting logic gates through the introduction of an additional sequestration reaction between the input and output chemical species of the gate. As a mechanism of study, we employ antisense RNAs (asRNAs) expressed alongside the mRNA (mRNA) of the logic gate within single transcripts. These asRNAs target mRNAs of adjacent gates and create additional feedback that supports the protein-mediated repression of the gates. Numerical and symbolic analysis indicates that the sequestration steepens the gate's dose-response curve, reduces leakage, and can potentially be used to adjust the location of logic transition. To leverage these effects, we demonstrate how design parameters can be tuned to obtain desired dose-response curves and outline how arbitrary combinational circuits can be assembled using the improved gates. Finally, we also discuss an implementation using split transcripts.
由转录抑制驱动的反向遗传逻辑门是遗传电路设计中已确立的构建模块。通常,这些门的剂量反应曲线需要剂量的大幅变化才能在逻辑开和关状态之间转换,这在连接门时可能会导致逻辑上不确定的中间状态。此外,关断状态下的泄漏是一个普遍问题,尤其是在电路的输出级。本研究探讨了通过在门的输入和输出化学物质之间引入额外的隔离反应来改进反向逻辑门的潜力。作为一种研究机制,我们在单个转录本中与逻辑门的信使核糖核酸(mRNA)一起表达反义RNA(asRNA)。这些asRNA靶向相邻门的mRNA,并产生额外的反馈,支持蛋白质介导的门抑制。数值和符号分析表明,隔离使门的剂量反应曲线变陡,减少了泄漏,并有可能用于调整逻辑转换的位置。为了利用这些效应,我们展示了如何调整设计参数以获得所需的剂量反应曲线,并概述了如何使用改进的门组装任意组合电路。最后,我们还讨论了使用分裂转录本的实现方式。