Folding of group I introns from bacteriophage T4 involves internalization of the catalytic core.
Fe(II)-EDTA, a solvent-based cleavage reagent that distinguishes between the inside and outside surfaces of a folded RNA molecule, has revealed some of the higher-order folding of the group IB intron from Tetrahymena thermophila pre-rRNA. This reagent has now been used to analyze the bacteriophage T4 sunY and td introns, both of which are members of the group IA subclass. Significant portions of the phylogenetically conserved secondary structure are protected from Fe(II)-EDTA cleavage. However, the P4 secondary structure element, which is substantially protected in the Tetrahymena intron, is available for cleavage in the two T4 introns. We conclude that a family of catalytic RNAs (ribozymes) that possess similar secondary structures and have similar activities fold into similar but nonidentical tertiary structures that nevertheless serve to internalize portions of the catalytic center. Furthermore, comparison of cleavage patterns of the sunY and td intron RNAs indicates that conserved nucleotides outside as well as within the catalytic core participate in the tertiary structure.
Heuer
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Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215.
Chandry
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Belfort
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Celander
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Cech
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TR
D000818:Animals; D001483:Base Sequence; D004492:Edetic Acid / Q000494:pharmacology; D004926:Escherichia coli / Q000235:genetics*; D005296:Ferrous Compounds / Q000494:pharmacology; D007438:Introns; D008969:Molecular Sequence Data; D008970:Molecular Weight; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry / Q000187:drug effects / Q000235:genetics*; D016337:RNA, Catalytic / Q000737:chemistry / Q000187:drug effects / Q000235:genetics*; D013604:T-Phages / Q000235:genetics*; D016808:Tetrahymena thermophila / Q000235:genetics*
D005296:Ferrous Compounds; D012322:RNA Precursors; D016337:RNA, Catalytic; C055526:Fe(II)-EDTA; D004492:Edetic Acid