A riboswitch is an RNA element in the 5′ leader of an mRNA that senses a small-molecule ligand directly — no protein sensor needed. It has two domains: an aptamer that binds the ligand, and an expression platform that folds into one of two mutually exclusive secondary structures depending on whether the aptamer is occupied. This 2D view adds a live plot of the Hill isotherm itself alongside the folding population.
Ligand binding (Hill isotherm):
θ = [L]^n / ([L]^n + Kd^n)
ON-switch: P(expression ON) = θ
OFF-switch: P(expression ON) = 1 − θ
Per-molecule folding (stochastic relaxation toward target P):
each mRNA flips state with rate k_fold · |P_target − state|
- [L] and Kd — set how much ligand is bound at equilibrium; θ is the standard binding isotherm used to fit real aptamer affinities (e.g. TPP, SAM, purine, synthetic theophylline riboswitches). Watch the marker slide along the curve in the top-right plot as you drag the slider.
- Hill coefficient n — models cooperative or multi-site ligand binding; steeper n gives a sharper, more switch-like curve in the plot, closer to a digital genetic switch.
- ON-switch vs OFF-switch — natural riboswitches are mostly OFF-switches (ligand triggers a terminator hairpin that halts transcription, or occludes the ribosome-binding site); engineered riboswitches (theophylline, synthetic aptazymes) are routinely built either way as a design choice.
- Folding rate — co-transcriptional folding is a race: each nascent mRNA only gets one chance to commit to a conformation as RNA polymerase transcribes past the decision point, so real riboswitches show kinetic — not just thermodynamic — control. Each glowing dot here represents one such mRNA molecule stochastically relaxing to the population's target ON-fraction.
Real-world relevance: synthetic riboswitches are used as small-molecule-inducible expression switches in metabolic engineering and cell therapy, letting an engineer turn a gene on or off by simply adding a chemical to the growth medium — no protein transcription factor required.
Drag the stage to pan, scroll (or pinch) to zoom.