@article {Rodrigo009688, author = {Guillermo Rodrigo and Satya Prakash and Shensi Shen and Eszter Majer and Jos{\'e}-Antonio Dar{\`o}s and Alfonso Jaramillo}, title = {Cooperative riboregulation in living cells through allosteric programming of toehold activation}, elocation-id = {009688}, year = {2014}, doi = {10.1101/009688}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2014/09/27/009688}, eprint = {https://www.biorxiv.org/content/early/2014/09/27/009688.full.pdf}, journal = {bioRxiv} }