Figure 1

Example on structure representations. A sequence, shown in A), folds into a structure that is represented by the three equivalent illustrations in B-D). The structure consists of a helix with three base pairs (ACC paired with GGU), a bulge loop (N--N; N meaning aNy nucleotide), and a helix with two base pairs formed by any complementary nucleotides. The dashes designate omitted sequence stretches. The structure in B) is in dot-bracket notation; that is, dots mark unpaired nucleotides and pairs of opening and closing brackets mark a base pair. The structure in C) is the usual squiggly representation. D) is the tree representation of the same structure: a stacked region (sr) is formed by an A:U pair stacked on top a bulge loop (bl) including two stacking pairs (C:G/C:G) and a loop region with one or more residues (r) on the left (5') side. The helix continues with a "closed" structural element (which is defined as any substructure starting with a base stack).