title: Evidence that alternate foldings of the hepatitis delta RNA confer varying rates of self-cleavage.
abstract: The pentapurine sequence GGAGA, located between 80 and 84 nucleotides downstream of the cleavage site in the self-cleaving antigenomic RNA of hepatitis delta virus, is necessary for highly efficient cleavage and for stability in up to 20 M formamide. Yet much of the cleavage activity lost upon its removal from the 3' end of an 84-nucleotide RNA can be restored by elongation of the 5' end of the RNA with the polypyrimidine sequence found in the virus. We propose that this sequence alteration causes a refolding of the RNA, resulting in a "structural compensation" of the active core of the molecule. Restoration of the self-cleavage activity did not restore the ability to cleave in high concentrations of formamide. Deletion mutagenesis was carried out and supported the alternate RNA folding. The ability to assume more than one active conformation and for one RNA structure to compensate for another in supporting ribozyme activity may be unique to RNA enzymes and could be a useful adaptation in viruses or in prebiotic RNAs.
authors.affiliation: Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104.
authors.forename: P A
authors.initials: PA
authors.lastname: Gottlieb
authors.forename: Y
authors.initials: Y
authors.lastname: Prasad
authors.forename: J B
authors.initials: JB
authors.lastname: Smith
authors.forename: A P
authors.initials: AP
authors.lastname: Williams
authors.forename: G
authors.initials: G
authors.lastname: Dinter-Gottlieb
mesh_terms: D001483:Base Sequence; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism*; D003698:Hepatitis Delta Virus / Q000378:metabolism*; D007700:Kinetics; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D017384:Sequence Deletion; D014158:Transcription, Genetic
chemical_list: D004279:DNA, Viral; D016337:RNA, Catalytic