258 Chapter 7
Figure 7.7 The secondary and tertiary structure of a loop–loop interaction. Coaxial stacking is preserved in a
“kissing loop” complex by the formation of a bend in the overall structure. (a) Schematic of a loop–loop
interaction. (b) Secondary structure of the ColE1 loop–loop interactions. (c) NMR structure of the
complex
(Reprinted for Ref. 74. © (1998), with permission from Elsevier)
Because of their ability to serve as both hydrogen-bond donors and acceptors, 2-OH groups can inter-
digitate at the interface between two RNA duplexes, resulting in ribose zippers. This essential mode of
RNA packing has been observed in the crystal structures of many large RNA molecules, and it is a core
motif within the hepatitis delta ribozyme active site (Figure 7.10).^13
7.1.4.1.1 Metal Ions in RNA Tertiary Structure. Most RNA tertiary structures are stabilized
by metal ions, particularly Mg^2 and K.14–16Metal ions can interact with RNA in at least four ways
(Figure 7.11).
- They can non-specifically screen the charge of the polyanionic backbone, thereby reducing
repulsion between RNA strands. - They can bind to specific RNA sites and, without forming specific interactions, provide local
stability to regions of strongly negative electrostatic potential.
Figure 7.6 The structure of tRNA. (a) Secondary structure. Bold dots indicate positions of paired bases. The identity
of conserved bases and functions of tRNA regions are indicated. Dashed lines represent tertiary interactions
in the three-dimensional structure. (b) Tertiary structure. Colours and labels differentiate the various
functional domains of the tRNA