Open AccessHigher order interactions in 23s rRNA.
Author(s) -
Niels Larsen
Publication year - 1992
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.89.11.5044
Subject(s) - ribosomal rna , rna , 23s ribosomal rna , phylogenetic tree , biology , protein secondary structure , genetics , protein subunit , nucleic acid secondary structure , base pair , nucleotide , computational biology , loop (graph theory) , ribosome , combinatorics , gene , biochemistry , mathematics
An alignment of 75 phylogenetically diverse large subunit ribosomal RNA sequences was created and searched for secondary and tertiary structure elements by computer. The search revealed four unknown secondary structural pairings, two internal loop closings, and five short-range tertiary interactions--two of which were pairings of an unusual type. One brings a loop together with two other loops previously known to be paired, and one involves a nucleotide within a presumed tetraloop. The latter interaction constrains the RNA structure near the ribosomal E-site, where two base pairs previously suggested to be in parallel orientation are now proven. No clear phylogenetic evidence for direct base pairing between the large and small subunit rRNA was found.