title: Efficient site-specific nonribozyme opening of hepatitis delta virus genomic RNA in infected livers.
abstract: Examination of the 1,679-nucleotide (nt) unit-length hepatitis delta virus (HDV) RNAs in the livers of two HDV-infected woodchucks showed that 96% of the antigenomic RNA but only 50% of the genomic RNA was circular. We subsequently found that at least half of the linear unit-length genomic RNA was open at a unique location. Using a modified form of RNA ligation-mediated amplification of cDNA ends, we showed that the 5' end was located at nt 1212. Like the previously described ribozyme cleavage site at nt 686, the new site produced a 5'-OH. Nevertheless, we showed that this novel site was not produced by activity of the HDV genomic ribozyme. We speculate that the 5' end at nt 1212 reflects a preferred site of posttranscriptional endonucleolytic cleavage of genomic RNA.
authors.affiliation: Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111-2497, USA.
authors.forename: J
authors.initials: J
authors.lastname: Chang
authors.forename: G
authors.initials: G
authors.lastname: Moraleda
authors.forename: S
authors.initials: S
authors.lastname: Gudima
authors.forename: J
authors.initials: J
authors.lastname: Taylor
mesh_terms: D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D016679:Genome, Viral; D003699:Hepatitis D / Q000473:pathology / Q000821:virology*; D003698:Hepatitis Delta Virus / Q000235:genetics* / Q000378:metabolism; D022521:Ligase Chain Reaction; D008099:Liver / Q000473:pathology / Q000821:virology*; D008392:Marmota; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*
chemical_list: D016337:RNA, Catalytic; D012367:RNA, Viral