4 - RNA Conformational Dynamics

Abstract

This chapter discusses various concepts of secondary structure formation in the RNA molecule. The RNA folding problem is four-dimensional. The spatial coordinates used to define the structures that RNA can take on are essential but not sufficient for a full understanding of molecular properties and function. In a living cell there is continuous RNA synthesis, folding, conformational change, and degradation. The time range covered is vast—from pico- and nanoseconds for structural changes in individual nucleotides, to microseconds for forming small hairpin helices, and to milliseconds for forming compact tertiary structures. Renaturation, or undoing incorrect RNA folds takes hours or days, or longer. The energy needed to stabilize double helical nucleic acids comes largely from the stacking the bases together. Because of the cooperative character of double helix formation, the dynamic and equilibrium properties of base pairs differ greatly depending on whether they are located at the end of a helix or in its interior. Base pairs at the end of a helix open and close rapidly in a process called “fraying,” which has an equilibrium constant of roughly 2–10, depending on the nature of the base pair and its neighbor. Further, the chapter also discusses tertiary structure dynamics, switch in stacking in the tRNA anticodon loop, and switching and docking of the PI Helix in a ribozyme in the chapter.