title: Three-dimensional folding of Tetrahymena thermophila rRNA IVS sequence: a proposal.
abstract: We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the theoretical analysis with a computer method previously proposed, to find optimal free energy secondary structures with the required features, under the suitable constrains. Then we tried folding the obtained secondary structures, in low resolution tertiary models, which kept up the proximity of the catalytic sites also in the space. The proposed tertiary folding seems to provide for a better explanation to the transesterification mechanisms and moreover it is in good agreement with the experimental data (activity of mutants, enzymatic cleavages, phylogenetically conserved regions).
authors.affiliation: Department of Chemistry, University of Rome I, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Benedetti
authors.forename: S
authors.initials: S
authors.lastname: Morosetti
mesh_terms: D000818:Animals; D007438:Introns; D008958:Models, Molecular; D009154:Mutation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012326:RNA Splicing; D016053:RNA, Protozoan / Q000737:chemistry*; D012335:RNA, Ribosomal / Q000737:chemistry*; D013768:Tetrahymena / Q000235:genetics*
chemical_list: D016053:RNA, Protozoan; D012335:RNA, Ribosomal; D012313:RNA