UNIT 12.1An Overview of RNA Structure Prediction and Applications to RNA Gene Prediction and RNAi Design

Chapter 12 describes methods for predicting RNA structures. The appreciation of the role of RNA in the cell continues to grow rapidly. Prior to 1982, RNA was thought to have three forms, each with a distinct function: mRNA contained the sequence of the gene to direct its synthesis into protein; tRNA was the adapter that connected the codons of the mRNA to the amino acids of the protein; and rRNA served as the structural scaffold upon which the ribosome formed, but it was assumed that the ribosomal proteins performed the functions of peptide synthesis. Tom Cech’s discovery of catalytic RNA was the first of many realizations of RNA’s importance and versatility. Since then, many additional RNA enzymatic activities have been discovered (Doudna and Cech, 2002), as well as many examples of RNAs importance in regulating gene expression (Gottesman, 2002; Stormo, 2003). The discovery that interfering RNAs (RNAi), both naturally occurring and designed, can greatly diminish the expression of a gene has led to new approaches for discovering the functions of genes and the consequences of their elimination (Zamore and Haley, 2005). It has also come to be appreciated that RNA can be selected in vitro to have many functions that may not exist in vivo