Switch

In EteRNA, a switch is a puzzle or  lab in which a small molecule binds to the sequence at a binding site, resulting in a change in the structures of the puzzle. One example molecule is FMN.  Theophylline is another.

A switch puzzle is a puzzle which requires you to design a sequence to stabilize two or three different states at the same time, with one or more states getting a little bonus negative energy to help it fold. (Hoglahoo)

The original Lab switches in EteRNA had 2 states; one target structure that RNA should fold into without the molecule, and another target structure that RNA should fold into when it is bound to the molecule. Later capability added 2 state puzzle creation ability in Puzzle Maker and the ability to have the molecule in both states. 3 state capability was also added.

 

EteRNA Game Switch Model

In a state where the molecule is present, the EteRNA calcuation of Free Energy gets an energy bonus when the molecule is correctly bound to the binding site (indicated by glows around nucleotides). This energy difference allows the game to have the RNA fold into different target structures with a single sequence based on where/if the molecule is bound. 

 

History: On Apr 10, 2012 a notice "Simple RNA Switch binding bonus increased" in EteRNA news announced that the FMN binding energy bonus would be increased from -2.1 to -4.86 kcal.