Molecular recognition characteristics of SAM-II aptamers. (a) In-line probing of A. tumefaciens 156 metA RNA in the presence of 1 mM SAM, SAH, SAC, and Met. See legend to Figure 3a for an explanation of the labels. (b) Chemical structures of SAM and a generalized SAM analogue. Arrows represent possible hydrogen bonds and electrostatic interactions that could serve as points of recognition by the aptamer. Circled interactions were determined to have strong (solid) or weak (dashed) contributions to binding affinity in singly substituted chemical analogues. Recognition of the N1 position of SAM was not tested. (c) Apparent Kd values of SAM analogues for binding to 156 metA. Columns (n, X, Y, Z, R1, R2, R3) correspond to groups on the core structure in (b). The S-methyl group (gray box) is not present for SAH and SAC.