General composition framework for ligand-controlled RNA regulatory systems

A method for rendering expression of a target gene in a cell dependent on the presence or absence of a molecule, comprising introducing into the cell a polynucleotide comprising:

• (1) a modular actuator domain comprising a substrate for RNase III, wherein said substrate, when processed by RNase III, produces an siRNA or miRNA that targets a transcript of said target gene,
• (2) a modular sensor domain that detects concentration or status change of the molecule, wherein the modular sensor domain comprises an aptamer,
• (3) an information transmission domain (ITD) between the modular actuator domain and the modular sensor domain, said information transmission domain comprising:
• (a) a general transmission region,
• (b) a switching strand, and,
• (c) a competing strand,
• wherein the switching strand and the competing strand are in a continuous sequence and compete to bind to the general transmission region through hybridization interactions,
• (i) wherein detection of the concentration or status change by the modular sensor domain, through binding of said molecule to said modular sensor domain, favors a conformation change in the modular actuator domain;
• (ii) wherein said conformation change is mediated by a strand-displacement mechanism in the ITD to favor the binding of the general transmission region to one of said switching strand and said competing strand;
• and wherein said hybridization interactions are sufficient to allow said conformation change to occur by the strand-displacement mechanism;
• and,
• (iii) wherein said conformation change modulates the ability of said substrate to be processed by RNase III to produce the siRNA or miRNA for targeting said transcript, at a rate dependent upon the presence or absence of said molecule.