Different local topologies can give rise to similar tertiary contacts in group I introns

<p><b>Copyright information:</b></p><p>Taken from "Searching genomes for ribozymes and riboswitches"</p><p>Genome Biology 2007;8(4):210-210.</p><p>Published online 30 Apr 2007</p><p>PMCID:PMC1895996.</p><p></p> 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. 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 ribozyme [95] this is via a three-way junction, in the ribozyme [96], it is via a large bend (this is not the natural junction, however), and in the ribozyme [97], it is via a kink-turn. Each motif has a different sequence and set of structural constraints [77,92]