Figure 9.

BC1 RNA DTE and CGG-repeat stem-loops: noncanonical motif structures. Noncanonical purine∙purine pairs are symbolized by ∙, standard WC pairs by = (GC) or – (AU), wobble WC pairs by ·. In the BC1 RNA DTE, the noncanonical GA core motif resides in an A-form helix that is part of the 5′ BC1 apical stem-loop domain (Muslimov et al., 2006; 2011). The GA core (red) is clamped by canonical base pairs which are mostly G=C standard WC (blue). The structure of the 5′ BC1 domain was established experimentally (Rozhdestvensky et al., 2001). In CGG-repeat stem-loops, noncanonical G∙G pairs (red) are flanked by G=C standard WC pairs (blue; Napierala et al., 2005; Zumwalt et al., 2007; Kiliszek et al., 2011). Noncanonical R∙R pairs (e.g. A∙G, G∙G) are rather strong, comparable in stability to A-U WC pairs (Mládek et al., 2009; Sobczak et al., 2010).