FIGURE 5-9 RNA secondary and tertiary structures. (a) Hairpins, stem-loops, and other secondary structures can form by base pairing between distant complementary segments of an RNA molecule. In stem-loops, the single-stranded loop between the base-paired helical stem may be hundreds or even thousands of nucleotides long, whereas in hairpins, the short turn may contain as few as four nucleotides. (b) Pseudoknots, one type of RNA tertiary structure, are formed by interaction of loops through base pairing between complementary bases. The structure shown forms the core domain of the human telomerase RNA. Left: Secondary-structure diagram with base-paired nucleotides in green and blue and single-stranded regions in red. Middle: Sequence of the telomerase RNA core domain, colored to correspond to the secondary-structure diagram at the left. Right: Diagram of the telomerase core domain structure determined by 2D-NMR, showing paired bases only and a tube for the sugar phosphate backbone, colored to correspond to the diagrams at left.

[Part (b) middle and right data from C. A. Theimer et al., 2005, Mol. Cell 17:671, PDB ID 1ymo.]