18 RNA Structural Elements and RNA Function

Abstract

The structural elements that now exist in RNA must have evolved to provide chemical stability and to facilitate their biological functions. Structural biologists believe that determining the conformation and stability of the structures adopted by RNA will provide a better understanding of their functions. This belief is based mainly on the success of Watson and Crick with double strands for DNA. Even this archetype only shows that complementary base-pairing makes replication easy; the details of helix twist and of A-form, B-form, … or Z-form geometry are less useful. Nevertheless, we continue to be optimistic and to study RNA structure in the hope that it will provide hints about how RNA does its many jobs. The main value of a structure is to suggest new experiments. The structure allows predictions about the effect of mutations, inhibitors, and enhancers, and about the mechanisms of the reactions. The overall goal is to learn the general features of RNA structure that can be inferred from the sequence and then to relate these structures to biological functions. It is important to recognize that a molecule is not a rigid object; structural elements are dynamic. Single-stranded loops are mobile, base pairs can form and break, and even base-paired helical regions can bend and flex. The presence or absence of structure depends not only on the sequence, but also on the temperature and the environment in general. This means that knowledge of the thermodynamics of structure formation is crucial (for review, see Turner and Bevilacqua, this volume).