From Eterna Wiki

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.

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 in Eterna