Predicted spacial location of the targeted upper stem residues and mutational design.
(A) Model for the 3D structure of the ε stem-loop. 3D structure prediction as implemented in the MC-Fold and MC-Sym program package  was combined with NMR-based structural information on the upper stem and apical loop (, PDB entry 2IXY) to derive a tentative model for the entire ε element with its lower stem (green), bulge (blue), upper stem (yellow) and apical loop (red). The same model is shown from two different angles to provide a visual impression of the spacial distribution of the targeted residues A1, A2, A9, A10, U13 and U15 (all in cyan). Their major groove location and close juxtaposition to the bulge and loop, respectively, is supported by the NMR data; other features, including the relative orientation of upper stem vs. lower stem, are arbitrary. (B) Specific mutations investigated. Nucleotide exchanges and their positions in a 2D representation of ε together with the designations of the mutants are indicated. A linear representation is shown in Table 1.