Figure 1.

Design and function of a binary RNA switch. (A) Modular rational design of TF1 RNA using five distinct RNA modules (numbered 1–5). Individual modules are depicted as an integrated sequence whose boundaries are schematically represented underneath. Communication modules cm⁺theo3 (15) and cm⁺FMN1 (13) are labeled theo3 and FMN1, respectively. Four putative ligand-dependent base pairs are labeled a–d. An arrowhead denotes the site of ribozyme cleavage. (B) Allosteric function of the TF1 RNA. Precursor RNA (Pre, internally ³²P-labeled) was incubated in the absence (–) or presence (+) of 1 mM theophylline (T) and/or 1 mM FMN (F) for 0 or 1 h. The region of gel containing the precursor and the 5′-cleavage fragment (Clv) is shown.