RNA Secondary Structures

Abstract

The three-dimensional structures of nucleic acids, RNA, and DNA, are dominated by double-helical regions that are formed by canonical Watson–Crick and wobble (GU) base pairs, which collectively are referred to as the secondary structure of the molecule. In the case of RNA, this level of description is of particular interest because it captures the thermodynamics of RNA folding quite well and allows a self-consistent description of folding dynamics. Furthermore, secondary structures are often evolutionarily well conserved, evolving much slower than the underlying sequences. From a bioinformatics perspective, RNAsecondary structures are a convenient representation because efficient exact algorithms are known to enumerate the structures that can be formed by a given sequence, to solve the folding problem, and to compute the partition function (and hence any thermodynamic quantity of interest) from a well-measured set of empirical energy parameters.