Tuning Ultrasensitivity in Genetic Logic Gates using Antisense RNA Feedback

Abstract

This work provides a study of a possible improvement of existing inverting genetic logic gates by introduction of a common sequestration reaction between their input and output chemical species. As a mechanism of study, we use antisense RNAs (asRNAs). The asRNAs are expressed with the existing messenger RNA (mRNA) of a logic gate in a single transcript and target mRNAs of adjacent gates, creating a feedback of the protein-mediated repression that implements the core function of the logic gates. The extended transcripts then share a common sequestration reaction mediated by the cellular host's RNA metabolism. This sequestration consists of double-stranded RNA (dsRNA) formation by asRNA and adjacent mRNA and subsequent degradation by the host. Numerical and stochastic analysis suggests that the feedback increases the steepness of the gate's transition region, reduces the leakage, and can potentially be used to adjust the transition location. To leverage these effects, we demonstrate how design parameters can be tuned to obtain desired dose-response curves and how arbitrary circuits can be assembled using the improved gates.