FIGURE 1.

Generalized L-platform/L-scaffold composite motif. Symbolic secondary structure (left) and cartoon-block schematic (right) representations of the generalized L-platform/L-scaffold. Residue numbering and base-pair symbols (Leontis and Westhof 2001; Leontis et al. 2002) are described in the Notation section. Strict conservation of nucleobase identity (e.g., for the general base guanine G5) is shown with bold font. Other nucleotides are shown with ambiguity characters representing apparent trends in preferred nucleobase identity across the ribozyme classes (e.g., N1, A2, and S3). The constituent elements of the L-platform (left: gray background; right: dotted “L”) motif are colored as follows: general base (G5) in blue, stacking/pairing “L” nucleotides (N-1, N4, and A6) in teal. The L-scaffold consists of the L-anchor (A2) in green, L-pocket nucleotide (S3) in yellow, and the scissile phosphate in magenta along with the interactions between those residues and the L-platform. The bulged N1 nucleotide is not colored as it does not generally play a specific functional role (with the exception of twister ribozymes).