Section 23.2.4.3. RNA

Although RNA and DNA are chemically similar, RNA presents a much greater variety of shapes and surfaces compared to the relatively simple B-form helix of DNA. Generally single-stranded, RNA often forms secondary structuresdriven by the base pairing of complementary stretches of sequence within the same strand. The formation of base-paired regions can result in stem loops, bulges and helices which can further assemble into more complicated tertiary structures, such as that observed for transfer RNAs. Protein-mediated recognition of RNA often depends as much on the three-dimensional structure presented by these secondary structures as on the specific identity of the base sequence.

Very little information is currently available on the structural details of protein–RNA interactions (Nagai, 1996). Only a handful of protein–RNA complex structures have been determined. These fall into three basic categories, depending on the secondary structure of the RNA: four tRNA–protein complexes, two stem-loop–protein complexes and a capped single-stranded RNA–protein complex.