Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch

(A) Ratio of number of counts for chamber b to chamber a in equilibrium dialysis for B. subtilis yitJ SAM-I riboswitch hybrid constructs of varying P1 and AT helix length (constructs constrained to form hybrids without any competing nucleotides) and the P2_AT construct in which the J1/2 region and the 5′ of the P1 helix are truncated. (B) Ratio of number of counts for chamber b to chamber a in equilibrium dialysis for B. subtilis yitJ SAM-I riboswitch hybrid constructs with competing nucleotides (6P1_10AT, 8P1_11AT) and non-base-pairing nucleotides (3p_10AT_5′GCC, 4P1_9AT_5′GAC).