Riboswitches

http://en.wikipedia.org/wiki/Riboswitch
Riboswitches are often conceptually divided into two parts: an aptamer and an expression platform. The aptamer directly binds the small molecule, and the expression platform undergoes structural changes in response to the changes in the aptamer. The expression platform is what regulates gene expression.
Expression platforms typically turn off gene expression in response to the small molecule, but some turn it on. The following riboswitch mechanisms have been experimentally demonstrated.

http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000823
Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures
Nicholas J. P. Wiebe, Irmtraud M. Meyer

• predict evolutionarily conserved helices that are likely to play a role in the co-transcriptional formation of the functional RNA structure(s) in vivo
• do not require a detailed knowledge of the in vivo environment, e.g. transcriptional speed, ion concentrations, interaction partners etc., and keep the number of free parameters and assumptions incorporated into the method to a minimum
• estimate reliability values for all predictions
• present a comprehensive performance evaluation
• have a performance which is robust with respect to sequence length 

Motivation.

If a structural feature is functionally important, it is typically well conserved in groups of related RNAs, even if the level of primary sequence conservation may be low.

One sequence can have multiple RNA secondary structures, transient structures