Figure 4

Different local topologies can give rise to similar tertiary contacts in group I introns. (a) The invariant core of a group I intron [36,94] is illustrated in schematic form with the paired segments indicated by P and the loop regions by L. The dashed lines indicate the contacts between the peripheral elements, which are indicated by the numbers in circles. (b) Three different group I introns illustrate distinct ways of achieving a similar tertiary contact (involving non-Watson-Crick A-minor base-base interactions between a GAAA tetraloop and two stacked pairs) connecting distant regions. In each case region 9 folds towards region 5 (as indicated by the shaded region) but, in the Twort ribozyme [95] this is via a three-way junction, in the Tetrahymena ribozyme [96], it is via a large bend (this is not the natural junction, however), and in the Azoarcus ribozyme [97], it is via a kink-turn. Each motif has a different sequence and set of structural constraints [77,92].