PT - JOURNAL ARTICLE AU - Guillermo Rodrigo AU - Satya Prakash AU - Shensi Shen AU - Eszter Majer AU - José-Antonio Daròs AU - Alfonso Jaramillo TI - Cooperative riboregulation in living cells through allosteric programming of toehold activation AID - 10.1101/009688 DP - 2014 Jan 01 TA - bioRxiv PG - 009688 4099 - http://biorxiv.org/content/early/2014/09/27/009688.short 4100 - http://biorxiv.org/content/early/2014/09/27/009688.full AB - Living cells rely on small non-coding RNAs (sRNAs) to regulate gene expression at the post-transcriptional level. Contrary to most protein-based activators of transcription, all known riboregulators do not exploit cooperative binding mechanisms to activate gene expression. We conceived a general strategy to design cooperative riboregulation by programming a hierarchical toehold activation cascade, which we implemented into a de novo sequence design algorithm. We engineered different riboregulatory systems relying on the conditional formation of a heterotrimeric species. We characterized the specificity of each RNA-RNA interaction in vitro and the cooperative activation of gene expression in Escherichia coli. As we only rely on a biochemical model to compute allosteric regulation, our strategy could be applied to reach more complex RNA-based nanostructures regulating gene expression for synthetic biology applications.