Investigating the structural basis of purine specificity in the structures of MS2 coat protein RNA translational operator hairpins

We have determined the structures of complexes between the phage MS2 coat protein and variants of the replicase translational operator In order to explore the sequence specificity of the RNA-protein Interaction. The 19-nt RNA hairpins studied have substitutions at two positions that have been shown to be important for specific binding. At one of these positions, -10, which Is a bulged adenosine (A) In the stem of the wild-type operator hairpin, substitutions were made with guanosine (G), cytidine (C) and two non-native bases, 2-aminopurine (2AP) and Inosine (1). At the other position, -7 in the hairpin loop, the native adenine was substituted with a cytidine. Of these, only the G-10, C-10 and C-7 variants showed interpretable density for the RNA hairpin. In spite of large differences in binding affinities, the structures of the variant complexes are very similar to the wild-type operator complex. For G-10 substitutions in hairpin variants that can form bulges at alternative places in the stem, the binding affinity is low and a partly disordered conformation is seen In the electron density maps. The affinity Is similar to that of wild-type when the base pairs adjacent to the bulged nucleotide are selected to avoid alternative conformations. Both purines bind in a very similar way in a packet in the protein. In the C-10 variant, which has very low affinity, the cytidine Is partly inserted In the protein pocket rather than intercalated In the RNA stem. Substitution of the wild-type adenosine at position -7 by pyrimidines gives strongly reduced affinities, but the structure of the C-7 complex shows that the base occupies the same position as the A-7 In the wild-type RNA. It is stacked in the RNA and makes no direct contact with the protein.