I have a two questions now; more may well come up.
Is the length of the reporter sequence highly constrained by the chemistry for fluorescence? I ask because if we believe in the NuPACK energy model, there isn’t much room for choice in a matching sequence of the switch that keeps it bound. This does not seem to be a problem with the initial TB input molecule and the single input case, but it could be a cause for concern when we get to multiple, novel, might be with some other input RNA(s). Having a few more bases in the reporter would give us more flexibility for balancing the energies between states
How is the reporter RNA linked to the fluorescent protein? In particular, will the protein fluoresce when the reporter RNA is bound to the switch RNA? Or not bound?