Internal transcribed spacer 1 of the yeast precursor ribosomal RNA. Higher order structure and common structural motifs

• Published in: Biochemistry (Easton) Vol. 29; no. 25; pp. 5911 - 5918
• Main Authors: Yeh, Lee Chuan C, Thweatt, Ray, Lee, John C
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 26.06.1990
• Subjects: Alkylating Agents - metabolism; Analytical, structural and metabolic biochemistry; arn; Autoradiography; Base Sequence; Biological and medical sciences; Carbodiimides - metabolism; CME-Carbodiimide - analogs & derivatives; Computer Simulation; Endoribonucleases - metabolism; Fundamental and applied biological sciences. Psychology; modele; modelos; Models, Chemical; Molecular Sequence Data; Nucleic Acid Conformation; Nucleic Acid Hybridization; Nucleic acids; Oligodeoxyribonucleotides; Ribonuclease T1 - metabolism; ribosomas; ribosome; ribosomes; rna; RNA Precursors - metabolism; Rna, ribonucleoproteins; RNA, Ribosomal - metabolism; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Sulfuric Acid Esters - metabolism; Transcription, Genetic - physiology; Modification; Nucleotide sequence; Transcription; Subunit; Secondary structure; Precursor; Fungi; Autoradiography; Ribosomal RNA; Ascomycetes; Models; Saccharomyces cerevisiae; Thallophyta
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00477a005

The higher order structure of the first internal transcribed spacer between the 18S and the 5.8S rRNA sequences in the Saccharomyces cerevisiae precursor ribosomal RNA has been investigated. Sites of potential base pairing in the RNA region have been determined by using a combination of enzymatic and chemical structure sensitive probes. Data generated have been used to evaluate secondary structure models predicted by minimum free energy calculations. Several alternative suboptimal structures were also evaluated. The derived model contains several stable hairpins. Theoretical secondary structural models for the corresponding RNA region from S. carlsbergensis, S. pombe, N. crassa, X. laevis, and mung bean have also been derived from identical calculations and assumptions. Certain structural motifs appear to be conserved despite extensive divergence in the base sequence. The yeast model should be a useful prototype for investigation of structure and function of precursor ribosomal RNA molecules.