title: Co-conservation of rRNA tetraloop sequences and helix length suggests involvement of the tetraloops in higher-order interactions.
abstract: Terminal loops containing four nucleotides (tetraloops) are common in structural RNAs, and they frequently conform to one of three sequence motifs, GNRA, UNCG, or CUUG. Here we compare available sequences and secondary structures for rRNAs from bacteria, and we show that helices capped by phylogenetically conserved GNRA loops display a strong tendency to be of conserved length. The simplest interpretation of this correlation is that the conserved GNRA loops are involved in higher-order interactions, intramolecular or intermolecular, 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 possibility that this type of tetraloop also takes part in higher-order interactions.
authors.affiliation: Department of Molecular Genetics, The University of Texas M.D. Anderson Cancer Center, Houston 77030-4095, USA. klas.h@mail.com
authors.forename: K O
authors.initials: KO
authors.lastname: Hedenstierna
authors.forename: J L
authors.initials: JL
authors.lastname: Siefert
authors.forename: G E
authors.initials: GE
authors.lastname: Fox
authors.forename: E J
authors.initials: EJ
authors.lastname: Murgola
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D009690:Nucleic Acid Conformation; D012335:RNA, Ribosomal / Q000737:chemistry*
chemical_list: D012335:RNA, Ribosomal