RNA compensation: A positive feedback insulation strategy for RNA-based networks

Abstract

The lack of signalling modularity of biomolecular systems poses major challenges toward engineering complex networks. An important problem is posed by the consumption of signaling molecules upon circuit interconnection, which makes it possible to control a downstream circuit but compromises the performance of the upstream circuit. This issue has been previously addressed with insulation strategies including high-gain negative feedback and phosphorylation-dephosphorylation reaction cycle. In this paper, we focus on RNA-based circuits and propose a new positive-feedback insulation strategy to mitigate signal consumption. An RNA input is added in tandem with transcription output to compensate the RNA consumption, leading to concentration robustness of the input RNA molecule regardless of the amount of downstream modules. We term this strategy RNA compensation, and it can be applied to systems that have a stringent input-output gain, such as Small Transcription Activating RNAs (STARs). Our analysis shows that RNA compensation not only eliminates the signaling consumption in individual STAR-based regulators, but also improves the composability of STAR cascades and the modularity of RNA bistable systems.