Co-conservation of rRNA tetraloop sequences and helix length suggests involvement of the tetraloops in higher-order interactions

Terminal loops containing four nucleotides (tetraloops) are common in struc tural RNAs, and they frequently conform to one of three sequence motifs, GN RA, UNCG, or CUUG. Hen we compare available sequences and secondary structu res for rRNAs from bacterial and we show that helices capped by phylogeneti cally conserved GNRA loops display a strong tendency to be of conserved len gth. The simplest interpretation of this correlation is that the conserved GNRA loops are involved in higher-order interactions, intramolecular or int ermolecular, resulting in a selective pressure for maintaining the lengths of these helices. A small number of conserved UNCG loops were also found to be associated with conserved length helices, consistent with the possibili ty that this type of tetraloop also takes part in higher-order interactions . (C) 2000 Societe francaise de biochimie et biologie moleculaire / Edition s scientifiques et medicales Elsevier SAS.