Predicting U-turns in ribosomal RNA with comparative sequence analysis

The U-turn is a well-known RNA motif characterized by a sharp reversal of t he RNA backbone following a single-stranded uridine base. in experimentally determined U-turn motifs; the nucleotides 3' to the turn are frequently in volved in tertiary interactions, rendering this motif particularly attracti ve in RNA modeling and functional studies. The U-turn signature is composed of an UNR sequence pattern flanked by a Y:Y, Y:A (Y = pyrimidine) or G:A b ase juxtaposition. We have identified 33 potential UNR-type U-turns and 25 related GNRA-type U-turns in a large set of aligned 16 S and 23 S rRNA sequ ences. U-turn candidates occur in hairpin loops (34 times) as well as in in ternal and multi-stem loops (24 times). These are classified into ten famil ies based on loop type, sequence pattern (UNR or GNRA) and the nature of th e closing base juxtaposition. In 13 cases, the bases on the 3' side of the turn, or on the immediate 5' side, are involved in tertiary covariations, m aking these sites strong candidates for tertiary interactions. (C) 2000 Aca demic Press.