- They can interact with RNA through “outer-sphere” contacts that are mediated by coordinated
water molecules (Figure 7.11a). - They can coordinate directly with RNA functional groups, particularly phosphate oxygens and base
heteroatoms (Figure 7.11b).
Because all four of these mechanisms are operative in most large RNA structures, it is often hard to
define the role of a particular metal ion. However, the locations of metal ions can be identified through
crystallography, NMR, or by biochemical studies involving metal-ion replacement, such as Mg^2 by ions
of the lanthanide Terbium(III).^17
A variety of RNA substructures serve as metal-ion binding sites. A-platforms are created by adjacent
A bases that lie side-by-side rather than stacking on one another (Figure 7.12a). The resultant flat plane
readily stacks on other nucleotides and results in a motif that is stabilized by direct interactions with a
potassium ion (Figure 7.12b).18,19
7.1.4.2 RNA Folding Pathways. How RNA molecules go from an unfolded to a folded state is called
the RNA foldingproblem.^20 It is remarkable that an RNA sequence contains sufficient information to
RNA Structure and Function 259
Figure 7.8 The tetraloop–receptor interaction in RNA tertiary structure. (a) A secondary structural diagram of the
tetraloop–receptor interaction. (b) Ribbon diagram from the crystal structure of the P456 domain of
a group I intron,^7 with the tetraloop–receptor interaction highlighted in red