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Riboswitches contain an aptamer domain, which is a highly specific metabolite-binding sensor, and an expression platform that acts as an effector for transcription or translation. The aptamer binds directly to metabolites like guanine, coenzyme B12, and lysine with high specificity. The expression platform responds to this binding by forming either an anti-terminator or terminator structure to regulate gene expression downstream.

When a metabolite binds to the aptamer at sufficient concentration, the expression platform converts from an anti-terminator to a terminator structure. This terminator, followed by uracil residues, causes RNA polymerase to dissociate from the mRNA and DNA template, terminating transcription. This mechanism allows riboswitches to shut down gene expression in response to high metabolite levels without requiring protein cofactors.

When a metabolite binds to the aptamer, the expression platform forms a hairpin structure that blocks the ribosome binding site, also known as the Shine-Dalgarno sequence. This prevents ribosome binding and blocks the initiation of translation. The riboswitch thus regulates protein synthesis by physically occluding the site where ribosomes must attach to begin translation.

Some riboswitches, like the glycine riboswitch, contain two separate aptamers that each bind the same metabolite. This dual-binding requirement means the riboswitch only functions when both metabolite molecules are bound, allowing it to sense only very high concentrations of the metabolite. Single-binding riboswitches like the lysine riboswitch respond to lower threshold concentrations with just one binding site.

Eukaryotic riboswitches regulate transcription through alternative splicing rather than transcription termination, because eukaryotic genes contain introns that separate transcription and translation. For example, TPP riboswitches in plants mask or expose splice sites in response to metabolite binding, producing either stable or unstable mRNA. This contrasts with prokaryotic riboswitches, which directly terminate transcription or block translation on the same transcript.

Some riboswitches, such as the glmS riboswitch-ribozyme, function as RNA enzymes that cleave the riboswitch mRNA when a metabolite is bound. After cleavage, the remaining mRNA is degraded by RNase, inhibiting translation. This ribozyme-based mechanism provides an alternative to terminator or anti-terminator structures for regulating gene expression in response to metabolite availability.

Riboswitch aptamers bind a diverse range of molecules with high specificity, including organic compounds like purines, coenzymes, and amino acids such as lysine and glycine. They also bind inorganic molecules including magnesium cations and fluoride anions. Most aptamers achieve this binding through hydrogen bonds or electrostatic interactions, allowing riboswitches to sense various metabolites and regulate their synthesis accordingly.