Design and analysis of a synthetic aptamer-based oscillator

We consider a realistic experimental implementation of a negative feedback molecular oscillator built with RNA aptamers proposed in our previous work [1]. This oscillator is composed of two synthetic genes interconnected through their RNA outputs. Regulation of transcription is achieved by controlling the activity of the enzymes rather than the activity of the promoters. We investigate the properties of the system's model analytically, checking if it has the appropriate structure to be an oscillator. Our analysis reveals that it is necessary to include an additional self-activation loop in the system to obtain a model with the structure of a candidate oscillator. We finally study this candidate oscillator with numerical simulations by randomly varying its parameters.