RNA structural motifs: building blocks of a modular biomolecule

Abstract

1. Introduction 2222. What is an RNA motif? 2222.1 Sequence vs. structural motifs 2222.2 RNA structural motifs 2232.3 RNA structural elements vs. motifs 2232.4 Specific recognition motifs 2242.5 Tools for identifying and classifying elements and motifs 2263. Types of RNA structural motifs 2283.1 Helices 2283.2 Hairpin loops 2283.3 Internal loops 2303.4 Junction loops/multiloops 2303.5 Binding motifs 2323.5.1 Metal binding 2323.5.2 Natural and selected aptamers 2343.6 Tertiary interactions 2344. Future directions 2365. Acknowledgments 2396. References 239RNAs 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.