### 10 The Interactions That Shape RNA Structure

#### Abstract

The noncovalent interactions important for shaping RNA during evolution are revealed by the RNA structures that occur naturally, and by thermodynamic measurements on model systems. First, we discuss the fundamentals of the molecular interactions, then the contributions of stacking, hydrogen-bonding, and metal ions to formation of helices and other motifs. Examples are given of how these interactions shape RNA structures. Finally, some speculations are presented as to how these interactions directed evolution. Since understanding of noncovalent interactions, and knowledge of three-dimensional structures of RNA, are limited, this chapter represents an early stage in the evolution of our understanding of how the two are connected.

FUNDAMENTALS

The equilibrium constant, *K*, relating the concentrations of two conformations, C_{1} and C_{2}, of an RNA strand is given by(1)K=[C1]/[C2]=exp(-ΔG°/RT)

For an association of two non-self-complementary strands A and B to give A·B, the relevant *K* = [A·B]/[A][B]. Here Δ*G*° is the standard free-energy difference between the two conformations, [C_{1}]/[C_{2}] and [A·B]/[A][B] are the ratios of the equilibrium concentrations, R is the gas constant (1.987 cal K^{−1} mole^{−1}), and *T* is the temperature in Kelvins. Thus, Changes in Δ*G*° of 1.4 and 2.8...

#### Full Text:

PDFDOI: http://dx.doi.org/10.1101/0.233-264