Figure 1.

Ciliate TER structure and pseudoknot sequence alterations. (A) The conserved core structure of ciliate TER determined by phylogenetic covariation and structural probing (4), highlighting the pseudoknot domain that forms into a quasicontinuous helix on stacking of the two stems, and the wild-type template sequence from T. thermophila. (B) Detail of the pseudoknot domain from T. thermophila with sequence, position numbers, and standard designations of stems 1 and 2 as well as loops 1 and 2. (C) Sequence alterations used within the pseudoknot domain. The top line shows the wild-type pseudoknot RNA sequence from T. thermophila. Specific changes are shown directly below the wild-type residues that have been changed. Comp 1 and Comp 2, compensatory mutations 1 and 2.