Biomod/2014/UCR/Breaking RNA

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RNA Clocks & Switches


RNA Animation v7.gif

Abstract

Biomolecular clocks and toggle switches are circuits with important roles in biological systems; for instance, oscillators direct circadian rhythms, and bistable circuits control many developmental pathways. We are building simple synthetic transcriptional in vitro oscillatory and bistable circuits using RNA aptamers. Similar circuits have been constructed in the past; however, our systems are the first to utilize RNA aptamers. These RNA aptamers regulate bacterial RNA polymerases’ activity to generate positive and negative feedback loops. We built numerical models, which show our systems exhibit the expected behaviors. Experimentally, we have shown that RNA polymerases can be inhibited and reactivated by the binding and removal of the aptamers through strand displacement. This is an important step towards experimentally validating our circuits. The simplicity of our design allows it to be easily built upon, thus, paving the way for new biological circuits where RNA aptamers are powerful, programmable tools for designing dynamic interactions.

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