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The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions.

The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (in color). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring.  Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix.

The adenine ring of SAM is the central position between five nucleotides.  The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position <scene name='82/824623/Nitrogenous_base_interactions/3'>Nucleotide Interaction</scene>(color).  

Most responses to stimuli are mediated by transcription factors that in some way either turn on or off the production of their regulatory target.  Genetic regulation by RNA is often used in bacterial cells.  In the use of the SAM riboswitch the aptamer of tertiary RNA will bind to the SAM ligand where the helices and nucleotides discussed before hold the ligand in place for productive binding and also folds around the tertiary RNA once binding takes place.  Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression.