CRYSTAL-STRUCTURE OF AN RNA DODECAMER CONTAINING THE ESCHERICHIA-COLISHINE-DALGARNO SEQUENCE

The synthetic dodecameric RNA fragment rUAAGGAGGUGAU resembles a regio n upstream of the initiation site in prokaryotic mRNAs whereas the pyr imidine-rich complementary strand is identical to the last 12 nucleoti des of Escherichia coli 16 S rRNA. The complex thus serves as a model for the Shine-Dalgarno interaction which is required for proper initia tion of translation. The crystal structure of rUAAGGAGGUGUA . rAUCACCU CCUUA has been determined at 2.6 Angstrom resolution and refined again st 2957 1 sigma(F) structure amplitudes to an X-value of 0.195. The un it cell of the triclinic crystals contains two double-stranded RNA mol ecules. The conformation of the two duplexes is similar, with a root-m ean-square deviation of 0.683 Angstrom between equivalent atoms, and r esembles calf thymus A-DNA as determined by X-ray fiber diffraction me thods. Both molecules from continuous helices that penetrate the entir e crystal, but the dinucleotide step in between dodecameric duplexes h as an unusual geometry with a negative twist angle. The long helices c ross over each other in a characteristic manner by inserting the backb one of one molecule into the minor groove of another. These contacts a re stabilized by several direct intermolecular hydrogen bonds most of which are mediated by 2'-hydroxyl groups of the ribose sugars suggesti ng a general mode for the interaction between RNA molecules which is d ifferent from DNA-DNA interactions.