De novo engineering RNA regulation in bacteria

Speaker: Alfonso Jaramillo

Abstract: The computational design of RNA interactions allows for the programming of complex information processing devices in bacteria. For this, we use evolutionary computation algorithms that automatically optimize the sequences of a RNA circuit by minimizing their interaction activation and formation energies. The recent engineering of self-assembly DNA interaction pathways in vitro by computational algorithms could not be extended to RNA in living cells until now. Here we report a general de novo RNA circuit design approach, where we have experimentally validated in E. coli fully synthetic RNAs displaying logic gate behavior. We also show in E. coli that our riboregulatory devices can be combined with known functional RNA fragments (such as ribozymes and aptamers) to create complex logic circuits in bacteria. We also characterized their in vivo RNA dynamics by using microfluidics time-lapse microscopy to track single-cells. Our work provides a new paradigm to design functional RNAs gates working in living cells by only utilizing first principles combined with a molecular interaction mechanism.