The four-base loops that cap many doublehelical structures in rRNA (the so-called "tetra-loops") exhibit highly invariant to highly variable sequences depending upon their location in the molecule. However, in the vast majority of these cases the sequence of a tetra-loop is independent of its location and conforms to one of three general motifs, GNRA, UNCG, and (more rarely) CUUG. For the most frequently varying of the 16S rRNA tetra-loops, that at position 83 (Escherichia col numbering), the three sequences CUUG, UUCG, and GCAA account for almost all examples encountered, and each of them has independently arisen at least a dozen times. The closing base pair of tetra-loop hairpins reflects the loop sequence, tending to be COG for UUCG loops and G-C for CUUG loops.The prediction of RNA structure from simple principles (e.g., base stacking energies) is an inexact art. Existing methods (1, 2) work acceptably well with simple molecules such as tRNAs, but with large molecules such as the rRNAs their utility is at best limited. However, higher-order structure for large RNAs can readily be inferred by the simple empirical approach of comparative (sequence) analysis, and the detailed secondary structures that now exist for the small-and large-subunit rRNAs attest to the approach's effectiveness (3-6).

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