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The structure of ribosomal RNA: a three-dimensional jigsaw puzzle.

The structure of ribosomal RNA and its role in protein biosynthesis has been the subject of intense investigation for many years, and interest in this field has received an added boost from the concept of the ribosomal RNAs as functional molecules in the ‘RNA world’. As a step towards trying to unravel the structures of these enormously complex molecules, a number of low-resolution models have been proposed for the three-dimensional folding of the 16S [1–6] and 23S [3, 7] RNA from the eubacterium Escherichia coli, based on various types of topographical information such as intra-RNA cross-linking or RNA—protein interaction data. All the models have in common that their starting point is the phylogenetically established secondary structure of the ribosomal RNA (e.g. [8, 9]), but they differ from one another both with respect to the topographical data sets used and with respect to the rules and assumptions applied to the three-dimensional folding process. As a result, the individual models show many similarities but also serious differences. The purpose of this article is both to summarize the structural data that are currently available and critically to discuss in general terms some of the principles and limitations involved in incorporating these data into the three-dimensional models.