1. Introduction 222

2. What is an RNA motif? 222

2.1 Sequence vs. structural motifs 222

2.2 RNA structural motifs 223

2.3 RNA structural elements vs. motifs 223

2.4 Specific recognition motifs 224

2.5 Tools for identifying and classifying elements and motifs 226

3. Types of RNA structural motifs 228

3.1 Helices 228

3.2 Hairpin loops 228

3.3 Internal loops 230

3.4 Junction loops/multiloops 230

3.5 Binding motifs 232

3.5.1 Metal binding 232

3.5.2 Natural and selected aptamers 234

3.6 Tertiary interactions 234

4. Future directions 236

5. Acknowledgments 239

6. References 239

RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common ‘structural elements’. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.