Physics-based design of RNA circuits in living cells

Living entities process information in very different ways than existing
human-made object as the former excel at having a built-in capability
for self-reproduction, self-construction, evolvability, self-organization, scalability, adaptability and robustness. They can store information in DNA or epigenetically, although the former case is more tractable, and hence exploitable, by current technology. The machinery of living cells allows expressing functional biomolecules encoded in DNA. Such biomolecules can further switch the expression of selected genes, progressing asynchronously through successive reaction steps. We propose a strategy for the design of logic gates in living
cells that relies on the expression of exogenous RNA as biomolecules.
The RNA has biophysical properties that allow engineering of complex logical devices by predicting the alternative conformations the RNA may adopt when interact with other RNA or small-molecules. Moreover, the devices can be connected once the RNA controls the expression of other RNAs. For this, we developed a methodology based on physical principles to automatically design RNA components able to transduce environmental signals into RNA, process the RNA throughout cascades of RNA
interactions to eventually regulate gene expression in cells. The gates
implement logic gates, RNA cascades and RNA-controlled RNA switches. Our
RNAs are different to any known non-coding sequence and their predicted
behaviour is validated in living E. coli at the population and single-cell levels. Moreover, we have developed switchable CRISPR/Cas9 guide RNAs able to sense RNAs and whole transcripts in vivo, which will
allow the de novo design of sensors for the cell-cycle phase or the tissue type in eukaryotic cells. Our RNAs could empower cells with a 'Virtual Machine', able to interpret a universal RNA language, allowing engineering networks of molecular switches that could be made to process arbitrary orders encoded in RNA.