2 - Thermodynamics of RNA Secondary Structure Formation

Abstract

This chapter covers the thermodynamics of RNA secondary structure motifs, describing the Watson–Crick helical regions, GU Pairs, and the loops in the Watson–Crick model. The first stage in predicting RNA structure is determination of secondary structure, essentially listing of base pairs contained in the folded structure. Determination of secondary structure also defines the various loops present in a given RNA. Often, these non-Watson–Crick regions of RNA are particularly important for functioning, since unusual arrays of functional groups are available there for tertiary interactions or recognition of other cellular components. Phylogenetic sequence comparison determines RNA secondary structure. When enough related sequences are not known, alternative methods are used, and the most popular is free energy minimization. It is based on two assumptions: (i.) the dominant interactions responsible for RNA structures are local, and (ii.) the conformations RNA adopts are in equilibrium—that is, they are the lowest free energy conformations. Rapid methods for the synthesis of oligonucleotides make it possible to study the sequence dependence of RNA secondary structure thermodynamics in a systematic way. Finally, the chapter discusses the environmental effects on RNA secondary structure thermodynamics.