SAM/SAH riboswitches. (a) SAM/SAH motif consensus diagram. Possible additional base-pairing interactions are shown (Additional File 1). The legend applies to all other consensus diagrams in this report. (b) Sequence and proposed secondary structure of SK209-52 RNA. In-line probing annotations are derived from the data in c. Asterisks identify G residues added to improve in vitro transcription yield. (c) In-line probing gel with lanes loaded with 5' 32P-labeled RNAs subjected to no reaction (NR), partial digestion with RNase T1 (T1), partial digest under alkaline pH (-OH), in-line probing reaction without added compound (-), or in-line probing reactions with various concentrations of SAM. Selected bands in the RNase T1 partial digest lane (products of cleavage 3' of G residues) are numbered according to the nucleotide positions in b. Uncleaved precursor (Pre) and two internucleotide linkages whose cleavage rates are strongly affected by SAM (3' of nucleotides 42 and 45) are marked. The full gel image is provided in Additional File 1. (d) Plot of the normalized fraction of RNAs whose cleavage sites (linkage 23 not shown in c ) have undergone modulation versus the concentration of SAM present during the in-line probing reaction. The curve represents an ideal one-to-one binding interaction with a KD of 8.6 μM.